Re: [Freesurfer] Registration: Variable Must Begin with a Letter Error

[dgw]

Hi Anderson,

Please supply the command input and the error as well as the previous 
correspondence.

Thanks
d

Sent from my Phone

> On Jan 26, 2017, at 16:10, Anderson Napolitano  
> wrote:
> 
> ​Thank you Dr. Greve and Don. Unfortunately adding '\' after spaces and 
> removing the spaces all together doesn't seem to resolve the said error. 
> 
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Re: [Freesurfer] Assign p value for every voxel and plot it in freeview

[dgw]

You haven't told us what you saved it as, but assuming whatever
software you used can save in .nii.gz or .mgz simply save as that.
Load the volume and change the colormap and opacity to your liking.

hth
d

On Tue, Jan 3, 2017 at 11:48 AM, Hao wen  wrote:
> Hello:
>
> I have a very simple question, after recon-all, I did some statistical
> analysis with some other softwares, so for example I got the p value for
> every voxel(volume_based),or p value for every vertex(surface-based), so I
> know how to map theses p values for surface-based pipeline, but for
> volume-based, how can we do that???
>
> I know that in FMRI pipeline, we can use the significance map(sig.nii) as
> the overlay,  but this is created by the group analysis(mri_glmfit), but can
> we created this sig.nii mannually and upload it to the oig.mgz and
> apar+aseg.mgz???
>
>
> Really need your help.
>
>
> Thanks in advance
>
>
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Re: [Freesurfer] Please send email only once as list, not each email

[dgw]

Hello Anand,

You control this in your subscription. Select digest instead of individual 
emails. Check the link at the bottom

Hth
D

Sent from my Phone

> On Dec 17, 2016, at 03:57, anand iyer  wrote:
> 
> Hello
> 
> I am signed up for receiving mails; and i get each individual one which is 
> flooding my inbox
> can you please send all only once a day as a list?
> 
> Thanks,
> Anand Iyer
> 
> 
> 
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Re: [Freesurfer] recon-all -s -localGI

[dgw]

André,

It looks like you have the matlab path typed correctly. I would try to
tab complete it in a terminal to check.
You currently have it typed as this:
/Applications/matlab/MATLAB_R2014a.app/bin/matlab
I expect it to be this on your computer:
/Applications/MATLAB_R2014a.app/bin/matlab

Try doing it through tab complete. then hit enter, if matlab opens
that is the correct path to add.

hth
d

On Wed, Dec 14, 2016 at 11:13 AM, André Schmidt  wrote:
> I get the following:
>
> Andres-MacBook-Pro:subjects andre$ getmatlab
> ERROR: Cannot find matlab.
> Does not exist or is not in path.
>
> I guess adding the path (or what I defined as path) didn't work.
>
> Bw
> André
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve
> [gr...@nmr.mgh.harvard.edu]
> Gesendet: Mittwoch, 14. Dezember 2016 17:03
>
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] recon-all -s  -localGI
>
> What happens if you run getmatlab ?
>
>
> On 12/14/16 7:14 AM, André Schmidt wrote:
>
> Dear Doug
>
> Thanks again for your help. I think I have added the path to my linux path.
> This is what I have done:
>
> Andres-MacBook-Pro:~ andre$ echo $PATH
> /Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin
> Andres-MacBook-Pro:~ andre$
> PATH=/Applications/fsl/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/Applications/matlab/MATLAB_R2014a.app/bin/matlab
> Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer
> Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>  freesurfer-Darwin-lion-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/subjects
> MNI_DIR   /Applications/freesurfer/mni
> FSL_DIR   /Applications/fsl/fsl
> Andres-MacBook-Pro:~ andre$ cd /Applications/freesurfer/subjects
> Andres-MacBook-Pro:subjects andre$ recon-all -s subj001 -localGI
> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
> Actual FREESURFER_HOME /Applications/freesurfer
> -rw-rw-r--  1 andre  staff  130383 Dec 14 11:44
> /Applications/freesurfer/subjects/subj001/scripts/recon-all.log
> Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar
> 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
> /Applications/freesurfer/subjects/subj001/surf
> #
> #@# Local Gyrification Index lh Wed Dec 14 13:15:53 GMT 2016
> \n mris_compute_lgi --i lh.pial \n
> ERROR: Matlab is required to run mris_compute_lgi!
> Darwin Andres-MacBook-Pro.local 12.6.0 Darwin Kernel Version 12.6.0: Wed Mar
> 18 16:23:48 PDT 2015; root:xnu-2050.48.19~1/RELEASE_X86_64 x86_64
>
> recon-all -s subj001 exited with ERRORS at Wed Dec 14 13:15:53 GMT 2016
>
> For more details, see the log file
> /Applications/freesurfer/subjects/subj001/scripts/recon-all.log
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
> I am still receiving the same error message. Do you have another clue what
> is going wrong here?
> Best wishes
> André
>
> 
> Von: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve
> [gr...@nmr.mgh.harvard.edu]
> Gesendet: Dienstag, 13. Dezember 2016 22:53
> An: freesurfer@nmr.mgh.harvard.edu
> Betreff: Re: [Freesurfer] recon-all -s  -localGI
>
> Is matlab in your linux path? On my mac, I had to add this path to my linux
> path:  /Applications/MATLAB_R2011b.app/bin/matlab
>
>
> On 12/13/16 11:16 AM, André Schmidt wrote:
>
> Many thanks for your help. According to your suggestion, I modified the
> start.up file in Users/andre/matlab/startup.m (see attached).
>
> However, I got the following error:
>
> Andres-MacBook-Pro:~ andre$ export FREESURFER_HOME=/Applications/freesurfer
> Andres-MacBook-Pro:~ andre$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
>  freesurfer-Darwin-lion-stable-pub-v5.3.0 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer
> FSFAST_HOME   /Applications/freesurfer/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/subjects
> MNI_DIR   /Applications/freesurfer/mni
> FSL_DIR   /Applications/fsl/fsl
> Andres-MacBook-Pro:~ andre$ cd /Applications/freesurfer/subjects
> Andres-MacBook-Pro:subjects andre$ recon-all -s subj001 -localGI
> Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0
> INFO: S

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

[dgw]

Marianna,

I think Doug means:

gr...@nmr.mgh.harvard.edu

hth
d

On Tue, Dec 6, 2016 at 10:32 AM, Marianna Riello  wrote:
> Yes I did it, I used your mail but it gives me an error.
> Check attachment.
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
> Sent: Tuesday, December 6, 2016 10:23 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>
> I did not. You should have had an opportunity to enter an email address of 
> the recipient. You can use my email
>
>
> On 12/5/16 6:35 PM, Marianna Riello wrote:
>> I uploaded the dicom mosaic on Martinos Center.
>> I am wondering whether you received it
>>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
>> Sent: Monday, December 5, 2016 12:13 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>
>> Can you upload the dicoms to
>> https://gate.nmr.mgh.harvard.edu/filedrop2
>>
>>
>> On 12/05/2016 12:09 PM, Marianna Riello wrote:
>>> Dear all,
>>>
>>> Thank you. I tried but still is showing the same error (check 2Error
>>> attachment) Do you have any other suggestions?
>>>
>>> Thanks in advance,
>>> Marianna
>>>
>>> -Original Message-
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N
>>> Greve
>>> Sent: Monday, December 5, 2016 12:00 PM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz
>>>
>>> Try not including the "-it dicom" arg and see if that works
>>>
>>>
>>> On 12/05/2016 10:01 AM, Marianna Riello wrote:
 Dear all again,

 Thanks for your reply.
 Please check the error attached when trying to convert the DICOM Mosaic in 
 .mgz file when using mri_convert.

 Thanks in advance,
 Marianna



 -Original Message-
 From: freesurfer-boun...@nmr.mgh.harvard.edu
 [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas
 N Greve
 Sent: Friday, December 2, 2016 12:17 PM
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

 It will handle mosaics (as the mosaics that fMRI data will come in).
 Hard to say what is going on without more specifics (command line,
 terminal output)


 On 12/02/2016 10:26 AM, Marianna Riello wrote:
> Dear all,
>
> I am wondering whether mri_convert can compute .mgz files for the
> reconstructions with the 'Mosaic Format SIEMENS DICOM files'.
>
> I have been computing .mgz with the enhanced format .dcm so far, and
> it always worked.
>
> I have used mri_convert to compute .mgz from .nii (I previously
> transformed the mosaic .dcm format in nifti with mricron but the
> reconstruction failed)
>
> Thanks in advance,
>
> Marianna
>
>
>
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>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>> Outgoing:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>>
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>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it 
>>> is addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail contains patient information, please contact the Partners Compliance 
>>> HelpLine at http://www.partners.org/complianceline . If the e-mail was sent 
>>> to you in error but does not contain patient information, please contact 
>>> the sender and properly dispose of the e-mail.
>>>
>>>
>>>
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>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/

Re: [Freesurfer] DTI Multi band sequence?

[dgw]

I can't remember the tag numbers, but I believe the time of slice
acquisition is in the dicom. You should be able to just pull that
field on one volume and compare the field for all slices and see if
any of them have the same time.

hth
d

On Wed, Nov 30, 2016 at 12:10 PM, Martin Juneja  wrote:
> Hi,
>
> I was wondering if there is any way in FreeSurfer/FSL/MATLAB to determine
> whether the DTI data (in DICOM format) I have is multi-band sequence?
>
> I used dicominfo in MATLAB but couldn't find any information related to
> multi-band in the dicom header.
>
> Any help would be really appreciated.
>
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Re: [Freesurfer] mapping ROI to surface space

[dgw]

another thing to check is that you are using a binary ROI file. The
Volume based image looked like it had a range of values.

hth
d

On Fri, Oct 28, 2016 at 10:53 AM, Bruce Fischl
 wrote:
> Hi Derek
>
> I think the dev version of mri_label2label supports open/close/dilate/erode
> operations:
>
> mri_label2label --help
> USAGE: mri_label2label.bin
>
>--srclabel input label file
>
>--erode  N erode the label N times before writing
>--open   N open the label N times before writing
>--close  N close the label N times before writing
>--dilate  Ndilate the label N times before writing
>  .
> .
> .
>
> if your version doesn't have these operations let us know and we can get you
> an updated one
>
> cheers
> Bruce
>
>
>
>
> On Fri, 28 Oct 2016, Andrews, Derek wrote:
>
>> Hi Bruce,
>>
>> As always thank you for your prompt reply.
>>
>> For the morphological close operation, would you suggest using mris_fill
>> on the surface ROI I created and then running mri_vol2surf again on the
>> volume output by mris_fill?
>>
>> Best, Derek
>>
>>
>> 
>> Derek Sayre Andrews, MSc
>> PhD Candidate
>>
>> The Sackler Institute for Translational Neurodevelopment
>> Department of Forensic and Neurodevelopmental Sciences
>> Institute of Psychiatry, Psychology & Neuroscience, King's College London
>>
>> Telephone: +44 (0)20 7848 5701
>> Email: derek.andr...@kcl.ac.uk
>>
>>
>>
>>
>>
>> On 28/10/2016 14:54, "Bruce Fischl"  wrote:
>>
>>> p.s. you could remove many/most of these holes using a morphological
>>> close operation
>>> On Fri, 28 Oct 2016, Andrews, Derek wrote:
>>>
 Hello Freesurfer Developers and Community,

 I am looking to map a ROI.nii based on the MNI152 template to the
 fsaverage
 pial surface.

 I have used the following commands

 Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl ‹12
 ‹t1

 Then

 mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh

 The ROI appears to be in the right place however is very blotchy. Have I
 missed a step? Or is this correct?

 See bellow a picture of the ROI highlighted in FSL and in tksurfer after
 mapped using the above.

 Thank you for your support,

 Best, Derek

 [IMAGE]





 _
 ___

 Derek Sayre Andrews, MSc
 PhD Candidate

 The Sackler Institute for Translational Neurodevelopment

 Department of Forensic and Neurodevelopmental Sciences

 Institute of Psychiatry, Psychology & Neuroscience, King's College
 London

 Telephone: +44 (0)20 7848 5701
 Email: derek.andr...@kcl.ac.uk



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Re: [Freesurfer] graphic board question

[dgw]

The last time I tried, I was using 5.1.0, but the graphics requirements 
are very modest and I don't believe they have increased. In the past 
there were some issues, with bad drivers on linux (I don't think this is 
an issue any longer on linux).

hth
d

On 10/14/16 10:57 AM, Dix Meiberth wrote:
> Thanks for your reply, did you use the newest release for your
> analyses?
>
> Best,
>
> DM
>
> -Ursprüngliche Nachricht- Von:
> freesurfer-boun...@nmr.mgh.harvard.edu
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von dgw
> Gesendet: Freitag, 14. Oktober 2016 16:24 An:
> freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] graphic
> board question
>
> The graphics card will not be an issue. I have used much slower
> integrated graphics without any problem.
>
> hth d
>
> On 10/14/16 9:05 AM, Dix Meiberth wrote:
>> Dear all,
>>
>>
>>
>> I'm thinking about starting a cortical thickness analysis.
>> Therefore I would like to buy a new machine, namely an Apple iMac
>> 21,5"
>>
>> including: 2,8 GHz Quad-Core Intel Core i5 (Turbo Boost up to 3,3
>> GHz); 8 GB 1867 MHz LPDDR3 RAM (on-board); Intel Iris Pro Graphics
>> 6200
>>
>>
>>
>> The Apple support told me that the graphic board may not be
>> sufficient to perform FS analyses as the Intel Iris Pro Graphics
>> 6200 card does not include an extern video memory.
>>
>> Does anyone of you has experience if the machine is in fact not
>> sufficient? Thanks in advance and
>>
>>
>>
>> best regards,
>>
>>
>>
>> DM
>>
>>
>>
>> ___ Freesurfer mailing
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>> The information in this e-mail is intended only for the person to
>> whom it is addressed. If you believe this e-mail was sent to you in
>> error and the e-mail contains patient information, please contact
>> the Partners Compliance HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to
>> you in error but does not contain patient information, please
>> contact the sender and properly dispose of the e-mail.
>>
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> list Freesurfer@nmr.mgh.harvard.edu
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>
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Re: [Freesurfer] graphic board question

[dgw]

The graphics card will not be an issue. I have used much slower 
integrated graphics without any problem.

hth
d

On 10/14/16 9:05 AM, Dix Meiberth wrote:
> Dear all,
>
>
>
> I’m thinking about starting a cortical thickness analysis. Therefore I
> would like to buy a new machine, namely an Apple iMac 21,5"
>
> including: 2,8 GHz Quad-Core Intel Core i5 (Turbo Boost up to 3,3 GHz);
> 8 GB 1867 MHz LPDDR3 RAM (on-board); Intel Iris Pro Graphics 6200
>
>
>
> The Apple support told me that the graphic board may not be sufficient
> to perform FS analyses as the Intel Iris Pro Graphics 6200 card does not
> include an extern video memory.
>
> Does anyone of you has experience if the machine is in fact not
> sufficient? Thanks in advance and
>
>
>
> best regards,
>
>
>
> DM
>
>
>
> ___
> Freesurfer mailing list
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] Co-registering different source data

[dgw]

I think you SUBJECTS_DIR might be set incorrectly,

/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label

I suspect the value should be:

/mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/

or possibly something else:

${SUBJECTS_DIR}/$SUBJECT/label/
should be the directory with Testing.label

hth
d

On 9/27/16 11:58 AM, Crawford, Anna wrote:
> Th output is below:
>
> aparc.annot.a2009s.ctab  lh.BA45.label   lh.V2.thresh.label   
>   rh.BA4p.label
> aparc.annot.ctab lh.BA45.thresh.label
> rh.aparc.a2009s.annot  rh.BA4p.thresh.label
> aparc.annot.DKTatlas40.ctab  lh.BA4a.label   rh.aparc.annot   
>   rh.BA6.label
> BA.ctab  lh.BA4a.thresh.label
> rh.aparc.DKTatlas40.annot  rh.BA6.thresh.label
> BA.thresh.ctab   lh.BA4p.label   rh.BA1.label 
>   rh.BA.annot
> lh.aparc.a2009s.annotlh.BA4p.thresh.labelrh.BA1.thresh.label  
>   rh.BA.thresh.annot
> lh.aparc.annot   lh.BA6.labelrh.BA2.label 
>   rh.cortex.label
> lh.aparc.DKTatlas40.annotlh.BA6.thresh.label rh.BA2.thresh.label  
>   rh.entorhinal_exvivo.label
> lh.BA1.label lh.BA.annot rh.BA3a.label
>   rh.MT.label
> lh.BA1.thresh.label  lh.BA.thresh.annot  rh.BA3a.thresh.label 
>   rh.MT.thresh.label
> lh.BA2.label lh.cortex.label rh.BA3b.label
>   rh.perirhinal.label
> lh.BA2.thresh.label  lh.entorhinal_exvivo.label  rh.BA3b.thresh.label 
>   rh.V1.label
> lh.BA3a.labellh.MT.label rh.BA44.label
>   rh.V1.thresh.label
> lh.BA3a.thresh.label lh.MT.thresh.label  rh.BA44.thresh.label 
>   rh.V2.label
> lh.BA3b.labellh.perirhinal.label rh.BA45.label
>   rh.V2.thresh.label
> lh.BA3b.thresh.label lh.V1.label rh.BA45.thresh.label 
>   Testing1.label
> lh.BA44.labellh.V1.thresh.label  rh.BA4a.label
>   Testing.label
> lh.BA44.thresh.label lh.V2.label rh.BA4a.thresh.label
>
> Thanks,
> Anna
> ________
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw 
> [dgwake...@gmail.com]
> Sent: Tuesday, September 27, 2016 11:52 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> what is the output of "ls"?
>
>
> On 9/27/16 11:50 AM, Crawford, Anna wrote:
>> Thank you. That worked for changing the default directory. When I run 
>> mri_label2label, I am still getting the same error that there is no such 
>> file or directory for the label.
>>
>> Anna
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw 
>> [dgwake...@gmail.com]
>> Sent: Tuesday, September 27, 2016 11:36 AM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Co-registering different source data
>>
>> Anna, if you are using bash the command is:
>>
>> export SUBJECTS_DIR=
>>
>>
>> On 9/27/16 11:31 AM, Crawford, Anna wrote:
>>> I also tried doing setenv SUBJECTS_DIR  but that did not work either.
>>>
>>> bash: setenv: command not found
>>>
>>> Thanks,
>>> Anna
>>> 
>>> From: Crawford, Anna
>>> Sent: Tuesday, September 27, 2016 11:12 AM
>>> To: Freesurfer support list
>>> Subject: RE: [Freesurfer] Co-registering different source data
>>>
>>> If I don't use --sd it uses the default subject directory (SUBJECTS_DIR
>>> /tools/freesurfer/subjects) which is not where my data is located.
>>>
>>> Thanks,
>>> Anna
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>>> [gr...@nmr.mgh.harvard.edu]
>>> Sent: Tuesday, September 27, 2016 10:50 AM
>>> To: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Co-registering different source data
>>>
>>> Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that
>>> is already set properly, then do not use the --sd.
>>>
>>>
>>> On 9/27/16 9:38 AM, Crawford, Anna wrote:
>>>> Hi,
>>

Re: [Freesurfer] Co-registering different source data

[dgw]

what is the output of "ls"?


On 9/27/16 11:50 AM, Crawford, Anna wrote:
> Thank you. That worked for changing the default directory. When I run 
> mri_label2label, I am still getting the same error that there is no such file 
> or directory for the label.
>
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of dgw 
> [dgwake...@gmail.com]
> Sent: Tuesday, September 27, 2016 11:36 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Co-registering different source data
>
> Anna, if you are using bash the command is:
>
> export SUBJECTS_DIR=
>
>
> On 9/27/16 11:31 AM, Crawford, Anna wrote:
>> I also tried doing setenv SUBJECTS_DIR  but that did not work either.
>>
>> bash: setenv: command not found
>>
>> Thanks,
>> Anna
>> 
>> From: Crawford, Anna
>> Sent: Tuesday, September 27, 2016 11:12 AM
>> To: Freesurfer support list
>> Subject: RE: [Freesurfer] Co-registering different source data
>>
>> If I don't use --sd it uses the default subject directory (SUBJECTS_DIR
>> /tools/freesurfer/subjects) which is not where my data is located.
>>
>> Thanks,
>> Anna
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Tuesday, September 27, 2016 10:50 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Co-registering different source data
>>
>> Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that
>> is already set properly, then do not use the --sd.
>>
>>
>> On 9/27/16 9:38 AM, Crawford, Anna wrote:
>>> Hi,
>>>
>>> I keep getting an error when I use mri_label2label. Below is my input and 
>>> output. I have tried various paths all the way down to the label and above 
>>> the subject level, but still always get the same error. I have also 
>>> verified it is the path with the label. Why is it not recognizing it?
>>>
>>> Thank you,
>>> Anna
>>>
>>>
>>> mri_label2label --sd 
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label  
>>> --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel 
>>> Testing1N.label --regmethod volume
>>>
>>> srclabel = Testing.label
>>> srcsubject = segfs
>>> trgsubject = segfs
>>> trglabel = Testing1N.label
>>> regmethod = volume
>>>
>>> usehash = 1
>>> Use ProjAbs  = 0, 0
>>> Use ProjFrac = 0, 0
>>> DoPaint 0
>>>
>>> SUBJECTS_DIR
>>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
>>> FREESURFER_HOME /tools/freesurfer
>>> Loading source label.
>>> No such file or directory
>>> mri_label2label: could not open label file Testing.label
>>> No such file or directory
>>> ERROR reading Testing.label
>>>
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Monday, September 26, 2016 6:20 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Co-registering different source data
>>>
>>> Hi Anna
>>>
>>> freeview now checks (in the dev version I believe) if the label has been
>>> sampled onto the surface and won't crash, but you need to use
>>> mri_label2label to sample it onto the surface before loading it onto the
>>> inflated surface in freeview
>>>
>>> cheers
>>> Bruce
>>>
>>>
>>> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>>>
>>>> Hi,
>>>>
>>>> i created a test ROI which saves as a label. Every time I try to load it 
>>>> as a label on the surface (inflated), it crashed FreeView. I'm not sure 
>>>> why it won't load there. I noticed this happens with some other ore-made 
>>>> labels as well. What could be the cause of this?
>>>>
>>>> I also tried doing mri_label2vol (to then do vol2surf), but I am getting 
>>>> an errorL option unknown. I did the following:
>>>>
>>>> mri_label2vol \  --label Testing.label \ --temp ../mri/brainmask.mgz
>>>

Re: [Freesurfer] Co-registering different source data

[dgw]

Anna, if you are using bash the command is:

export SUBJECTS_DIR=


On 9/27/16 11:31 AM, Crawford, Anna wrote:
> I also tried doing setenv SUBJECTS_DIR  but that did not work either.
>
> bash: setenv: command not found
>
> Thanks,
> Anna
> 
> From: Crawford, Anna
> Sent: Tuesday, September 27, 2016 11:12 AM
> To: Freesurfer support list
> Subject: RE: [Freesurfer] Co-registering different source data
>
> If I don't use --sd it uses the default subject directory (SUBJECTS_DIR
> /tools/freesurfer/subjects) which is not where my data is located.
>
> Thanks,
> Anna
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Tuesday, September 27, 2016 10:50 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Co-registering different source data
>
> Do you need to use the ---sd option? That sets the SUBJECTS_DIR. If that
> is already set properly, then do not use the --sd.
>
>
> On 9/27/16 9:38 AM, Crawford, Anna wrote:
>> Hi,
>>
>> I keep getting an error when I use mri_label2label. Below is my input and 
>> output. I have tried various paths all the way down to the label and above 
>> the subject level, but still always get the same error. I have also verified 
>> it is the path with the label. Why is it not recognizing it?
>>
>> Thank you,
>> Anna
>>
>>
>> mri_label2label --sd 
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label  
>> --srcsubject segfs --srclabel Testing.label --trgsubject segfs --trglabel 
>> Testing1N.label --regmethod volume
>>
>> srclabel = Testing.label
>> srcsubject = segfs
>> trgsubject = segfs
>> trglabel = Testing1N.label
>> regmethod = volume
>>
>> usehash = 1
>> Use ProjAbs  = 0, 0
>> Use ProjFrac = 0, 0
>> DoPaint 0
>>
>> SUBJECTS_DIR
>> /mnt/netScratch/crawforda/BrainStem/study11074/S2sdt/segfs/label
>> FREESURFER_HOME /tools/freesurfer
>> Loading source label.
>> No such file or directory
>> mri_label2label: could not open label file Testing.label
>> No such file or directory
>> ERROR reading Testing.label
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Sent: Monday, September 26, 2016 6:20 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Co-registering different source data
>>
>> Hi Anna
>>
>> freeview now checks (in the dev version I believe) if the label has been
>> sampled onto the surface and won't crash, but you need to use
>> mri_label2label to sample it onto the surface before loading it onto the
>> inflated surface in freeview
>>
>> cheers
>> Bruce
>>
>>
>> On Mon, 26 Sep 2016, Crawford, Anna wrote:
>>
>>> Hi,
>>>
>>> i created a test ROI which saves as a label. Every time I try to load it as 
>>> a label on the surface (inflated), it crashed FreeView. I'm not sure why it 
>>> won't load there. I noticed this happens with some other ore-made labels as 
>>> well. What could be the cause of this?
>>>
>>> I also tried doing mri_label2vol (to then do vol2surf), but I am getting an 
>>> errorL option unknown. I did the following:
>>>
>>> mri_label2vol \  --label Testing.label \ --temp ../mri/brainmask.mgz
>>>
>>> among other similar variations. Am I just inputting it wrong or am I just 
>>> missing information?
>>>
>>> Thank you,
>>> Anna
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
>>> [fis...@nmr.mgh.harvard.edu]
>>> Sent: Monday, September 26, 2016 4:23 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Co-registering different source data
>>>
>>> Hi Anna
>>>
>>> scuba is very old and deprecated. Try using freeview instead
>>>
>>> cheers
>>> Bruce
>>> On Mon, 26 Sep
>>> 2016, Crawford, Anna wrote:
>>>
 To create the volume ROI, I found something that said to use:

 scuba -v $filename

 to then make a new ROI.

 I got en error that I could not open scuba. Is this the correct way to go 
 about this, or is there some other means that I should be doing not 
 'scuba'?

 Thank you,
 Anna
 
 From: freesurfer-boun...@nmr.mgh.harvard.edu 
 [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl 
 [fis...@nmr.mgh.harvard.edu]
 Sent: Monday, September 26, 2016 1:52 PM
 To: Freesurfer support list
 Subject: Re: [Freesurfer] Co-registering different source data

 yes, create a volume ROI and you can map it onto the surface using
 mri_vol2surf

 cheers
 Bruce
 On Mon, 26 Sep 2016, Crawford, Anna wrote:

> For now, I am just trying to get any arbitrary ROI that I define. (I'm 
> new to this and am just tryin

Re: [Freesurfer] Coordinates of particular volumes

[dgw]

Aziz,

Try this:
[i,j,k]=find(mri.vol==17)

and get rid of the ind2sub call

hth
d

On Tue, Sep 27, 2016 at 2:00 AM, Aziz Nanthaamornphong
 wrote:
> I have tried to get the coordinates with following commands:
>
> mri = MRIread('aseg.mgz');
> pos = find(mri.vol == 17);
> [i,j,k] = ind2sub(10213,pos);
>
> However, I found that all values of 'j' are 1. is there something wrongs
> with my strategy?
>
> Best Regards,
> Aziz.
>
> On Mon, Sep 12, 2016 at 8:40 PM, Bruce Fischl 
> wrote:
>>
>> Hi Aziz,
>>
>> make sure $FREESURFER_HOME/matlab is in your matlab path.
>>
>> cheers
>> Bruce
>>
>> On Mon, 12 Sep 2016, Aziz Nanthaamornphong wrote:
>>
>>>
>>> Which the version of Matlab has a 'MRIread' function? I got this error
>>> message from my installed Matlab (v. 8.4.0).
>>> "Undefined function 'MRIread' for input arguments of type 'char'."
>>>
>>> Best Regards,
>>> Aziz.
>>>
>>> On Mon, Sep 5, 2016 at 6:46 AM, Bruce Fischl 
>>> wrote:
>>>   yup, or mri_Info called form the command line. If you use
>>>   MRIread on the aseg.mgz you can extract e.g. the left
>>>   hippocampus using matlab via:
>>>
>>>
>>>   mri = MRIread('aseg.mgz');
>>>   find(mri.vol == 17);
>>>   then compute the ras coords of those indices using ind2sub
>>>
>>>   cheers
>>>   Bruce
>>>
>>>   On Sun, 4 Sep 2016, Ruyuan Zhang wrote:
>>>
>>>
>>> Hi, Aziz
>>>
>>>  You can use MRIread function to read in a
>>> volume (i.e. brainmask.mgz).
>>> You will get a structure, which contains a field
>>> called ras2vox.
>>>
>>> cheers
>>>
>>> ruyuan
>>>
>>> On 9/4/16 6:23 PM, Aziz Nanthaamornphong wrote:
>>>   Hi,
>>> For example, I want to know the list of x, y, z
>>> coordinates of a left
>>> hippocampus volume.
>>>
>>> As you mentioned "ras2vox" matrices, hoe can I see
>>> or get these
>>> matrices?
>>>
>>> Thank you.
>>> Aziz
>>>
>>> On Monday, 5 September 2016, Bruce Fischl
>>> 
>>> wrote:
>>>   Hi Aziz
>>>
>>>   can you elaborate? What coordinates do you
>>> want? What are
>>>   you trying to do with them? The .mgz format
>>> contains
>>>   ras2vox matrices that let you go from voxel
>>> indices to RAS
>>>   coordinates and such.
>>>
>>>
>>>   cheers
>>>   Bruce
>>>
>>>
>>>   On Sun, 4 Sep 2016, Aziz Nanthaamornphong
>>> wrote:
>>>
>>> Dear Freesurfer experts,
>>> How can we get the coordinates (X, Y, Z)
>>> of a
>>> particular volume? I couldn't
>>> find any functions or command to do
>>> that.
>>>
>>> Thank you in advance.
>>>
>>> Aziz.
>>>
>>>
>>>
>>>
>>> --
>>>
>>> Aziz Nanthaamornphong, Ph.D.,
>>> Chair of Master of Science Program in Information
>>> Technology
>>> Department of ICT
>>> Faculty of Technology and Environment
>>> Prince of Songkla University, Phuket Campus
>>> +66 7627 6716 (v)
>>> http://research.te.psu.ac.th/aziz
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for
>>> the person to whom it is
>>> addressed. If you believe this e-mail was sent to
>>> you in error and the e-mai
>>> l
>>> contains patient information, please contact the
>>> Partners Compliance HelpLin
>>> e at
>>> http://www.partners.org/complianceline . If the
>>> e-mail was sent to you in er
>>> ror
>>> but does not contain patient information, please
>>> contact the sender and prop
>>> erly
>>> dispose of the e-mail.
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contac

Re: [Freesurfer] New way of installing and running Freesurfer - containers

[dgw]

Hi Chris,

This sounds great! How does it deal with the FreeSurfer license? I
know that the FreeSurfer team depends on licenses to keep track of the
number of users (a key component to justifying their work when
applying for grants). I'm looking forward to trying it out!

Thanks,
Dan

On Tue, Aug 9, 2016 at 12:37 PM, Chris Filo Gorgolewski
 wrote:
> Dear all,
> I have created a Docker image with Freesurfer distribution (and all required
> dependencies).
>
> Features:
>
> Only requires Docker to run (works on Linux, Mac and Windows - does not
> suffer from the VirtualBox bug)
> understands BIDS formatted datasets
> performs recon-all on all subjects
> allows you to run each subject independently (and potentially in parallel)
> automatically performs longitudinal analysis when multiple sessions are
> detected
> creates custom group level template for your study
> can be easily converted to a Singularity image using docker2singularity tool
> and run on your local HPC/cluster
>
> You can find more information here: https://github.com/BIDS-Apps/freesurfer
>
> Please let me know what do you think!
>
> Best,
> Chris
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
___
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Re: [Freesurfer] Obtaining White and pial surface maps for multiple subjects

[dgw]

Hi Vasudev,

I think a good place to start would be the wiki: 
surfer.nmr.mgh.harvard.edu/fswiki

Read through and then go through some of the tutorials.

hth
d

On 7/15/16 8:26 AM, Dev vasu wrote:
> Dear sir,
>
> I would like to know how could i possibly generate white and pial
> surface data for pool of 50 subjects ( 25 healthy controls and 2
> subjects with BLVP) using free surfer.
>
>
> Thanks
> Vasudev
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] Beta-Zero Correction - No Phase File

[dgw]

If both phase and magnitude data are there, you could use fslroi to 
separate the images out into two separate files.

hth
d

On 7/14/16 9:52 AM, Afzal, Afsana wrote:
> Hi,
>
> Just wanted to follow up on the issue of just having one fieldmap file
> for beta-zero correction outlined below.
>
> Thanks for your help,
>
> Afsana
>
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana
> [aaf...@mgh.harvard.edu]
> *Sent:* Tuesday, July 12, 2016 2:29 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* [Freesurfer] Beta-Zero Correction - No Phase File
>
> Hi,
>
> I'm working with a dataset that outputs only one file (not two separate
> mag and phase files) for the fieldmap. The data was also collected on
> non-Siemens scanners: Philips Ingenia and GE SIGNA HDx (not sure if this
> is the reason the fieldmaps are unpacking differently). I've attached
> the .dat file for one of the fieldmaps in this email.
>
> If there a way to separate out the mag and phase from the single
> fieldmap file so I can use epidewarp.fsl?
>
> Thanks,
>
> Afsana
>
> __
> *Afsana Afzal*
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
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Re: [Freesurfer] Error with MatlabR2016a and LGI

[dgw]

try this instead
PATH=/Applications/MATLAB_R2016a.app/bin/
export PATH

If it still doesn't work what is the output of `which matlab`
hth
d

On Fri, Jul 8, 2016 at 11:45 AM, Mahtab Farahbakhsh
 wrote:
> Dear FreeSurfer,
>
> I am trying to calculate LGI for my images, but it seems like that it
> doesn't work. I have tried everything, but it's still giving me the same
> error.
>
> I'm using FreeSurfer on a mac and my Matlab version is R2016a.
>
> When I try to run "recon-all -s  -localGI", I get this error: ERROR:
> Matlab is required to run mris_compute_lgi!.
>
> I have done these so far:
> PATH=/Applications/MATLAB_R2016a.app/bin/matlab:$PATH
> export PATH
>
> And my $PATH is:
> /Applications/MATLAB_R2016a.app/bin/matlab:/usr/local/fsl/bin:/Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/opt/X11/bin:
> No such file or directory
>
> And when I write getmatlab, I get this:
> ERROR: Cannot find matlab.
> Does not exist or is not in path.
>
> My original Matlab is in the /Applications folder and I also have a folder
> named "matlab" in my FreeSurfer folder.
>
> Would you please guide me what I should do?
>
> Best Regards,
> Mahtab.
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
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Re: [Freesurfer] Recon-all error after El Capitain update

[dgw]

It's hard to fully diagnose, without the command you called, but it
looks like you have your SUBJECTS_DIR and SUBJECT variable wrong, and
perhaps command syntax. Take another look at your command.

hth
d

On Thu, Jul 7, 2016 at 2:59 AM,   wrote:
> Hi list,
>
> after update with El Capitain, recon-all -all produce the error reported
> below.
>
>
> Thanks
>
> srclabel =
> /Applications/freesurfer/subjects/subject_prova/subj/fsaverage/label/lh.BA1.label
>
> srcsubject = fsaverage
>
> trgsubject = SUBJECTS_DIR
>
> trglabel = ./lh.BA1.label
>
> regmethod = surface
>
>
> srchemi = lh
>
> trghemi = lh
>
> trgsurface = white
>
> srcsurfreg = sphere.reg
>
> trgsurfreg = sphere.reg
>
> usehash = 1
>
> Use ProjAbs  = 0, 0
>
> Use ProjFrac = 0, 0
>
> DoPaint 0
>
>
> SUBJECTS_DIR/Applications/freesurfer/subjects/subject_prova/subj
>
> FREESURFER_HOME /Applications/freesurfer
>
> Loading source label.
>
> No such file or directory
>
> ERROR reading
> /Applications/freesurfer/subjects/subject_prova/Control89/fsaverage/label/lh.BA1.label
>
> Darwin iMac-di-Stefano.local 15.5.0 Darwin Kernel Version 15.5.0:
> root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64
>
>
> recon-all -s SUBJECTS_DIR exited with ERRORS
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
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Re: [Freesurfer] Order of overlays

[dgw]

You can also do this now, by simply changing the alpha level of the
colors in the CLUT, (note this only works in the dev version).

hth
d

On Sat, Jul 2, 2016 at 1:46 PM, Douglas Greve  wrote:
> Yes, you can. If I remember correctly, you can goto view->configure overlay,
> then find the item to specify that you want the labels under the activation.
>
>
> On 6/29/16 5:22 AM, Reza Rajimehr wrote:
>
> Hi,
>
> In Tksurfer, we want to show functional activity map and borders of aparc on
> a surface. The borders of aparc are always drawn on top of the activity map,
> which sometimes hide small activation blobs. Is it possible to draw the
> activity map on top of the aparc borders?
>
> Reza
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
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Re: [Freesurfer] freeview display problem

[dgw]

Hi Tilak,

Do the colors match this:
https://en.wikipedia.org/wiki/GLX#/media/File:Xf86_glxgears.png

?

hth
d


On 6/28/16 3:46 PM, Ramtilak Gattu wrote:
> glxgears shows up a screen with three gear wheels in blue, pink and
> green and frame information rate being printed out on the command window.
>
> 
> *From:* Ramtilak Gattu
> *Sent:* Tuesday, June 28, 2016 2:55:32 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: freeview display problem
>
>
> Nope they dont look normal they are being displayed in some other colors
> like heat is showing up as blue , jet as green etc. Even when the
> surfaces are loaded up the color of the surfaces doesnt look right. when
> the surface yellow is chosen are red it is being displayed as blue.
>
>
> Thanks
>
>
> Regards
>
> Tilak
>
> 
> *From:* Ramtilak Gattu
> *Sent:* Tuesday, June 28, 2016 2:01:00 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: freeview display problem
>
>
> Hey Ruopeng,
>
>
> I still couldnt figure out whats going on the freeview display. I
> updated the Nvidia drivers but still its not displaying in gray scale.
>
>
> please help.
>
>
> thanks
>
>
> Regards
>
> Tilak
>
> 
> *From:* Ramtilak Gattu
> *Sent:* Friday, June 24, 2016 12:25:50 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: freeview display problem
>
>
> That is all . No error messages at all.
>
> 
> *From:* Ramtilak Gattu
> *Sent:* Friday, June 24, 2016 10:25:42 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: freeview display problem
>
>
> I tried updating my Nvidia drivers. but now whenever I try to open
> freeview it says " aborted ( core dumped).
>
>
> please help.
>
>
> Thanks
>
>
> Regards
>
> Tilak
>
> 
> *From:* Ramtilak Gattu
> *Sent:* Thursday, June 23, 2016 5:27:12 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: freeview display problem
>
>
> May be thats the problem. I'll try to give it a shot to see if it fixes
> the problem.
>
>
> Thanks.
>
> 
> *From:* Ramtilak Gattu
> *Sent:* Thursday, June 23, 2016 4:10:28 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: freeview display problem
>
>
> This issue is only with freesurfer , images on fslview doesnt have this
> problem.
>
>
>
> 
> *From:* Ramtilak Gattu
> *Sent:* Thursday, June 23, 2016 3:31:41 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: freeview display problem
>
>
> That is just one layer the yellow contrast is from when we tune the
> contrast up or down.
>
> 
> *From:* Ramtilak Gattu
> *Sent:* Thursday, June 23, 2016 2:37:36 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* freeview display problem
>
>
> Hello ,
>
>
> I am having strange freeview display problem. The images doesnt appear
> in gray scale anymore. Please have a look at the attachment.  Is there a
> switch that was  turned on that I am not aware of.
>
>
> Could some one help.
>
>
> Thanks
>
>
> Regards
> Tilak
>
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
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Re: [Freesurfer] Fwd: Getting the pial surface to cover the entire medial temporal lobe structures

[dgw]

I would try Bruce's idea first, but another option would be to run
mri_tesselate on the aseg volume you had loaded in those images.

hth
d

On Wed, Jun 15, 2016 at 4:46 PM, Bruce Fischl
 wrote:
> Hi David
>
> we don't have anything that does this by default, sorry. If you don't care
> about the location of the white surface you could try setting all the voxels
> in the wm.mgz that are left or right hippo/amygdala in the aseg to 255 then
> running from autorecon2-wm forward.
>
> cheers
> Bruce
>
>
>
> On Wed, 15 Jun 2016, David Groppe wrote:
>
>>
>> Dear Free Surfers,
>>  I am using FreeSurfer's pial surface to map ECoG electrodes onto the
>> FreeSurfer average brain for group analyses via these two methods:
>>
>> Dykstra, A. R., Chan, A. M., Quinn, B. T., Zepeda, R., Keller, C. J.,
>> Cormier, J., et al. (2011). Individualized localization and cortical
>> surface-based registration of intracranial electrodes. NeuroImage, 1–42.
>> http://doi.org/10.1016/j.neuroimage.2011.11.046
>>
>>
>> Yang, A. I., Wang, X., Doyle, W. K., Halgren, E., Carlson, C., Belcher, T.
>> L., et al. (2012). Localization of dense intracranial electrode arrays
>> using
>> magnetic resonance imaging. NeuroImage, 63(1), 157–165.
>> http://doi.org/10.1016/j.neuroimage.2012.06.039
>>
>>
>> The methods work great. However, we've noticed that the pial surface
>> typically underestimates the extent of the amygdala and hippocampus (see
>> attached example images from FreeSurfer's demo Bert subject) where we
>> often
>> have electrodes. I understand that FreeSurfer does this by design, since
>> the
>> amygdala and hippocampus are not neocortex. However, is there a way to
>> force
>> the pial surface to include those medial temporal lobe structures for our
>> purposes? I tried "mris_make_surfaces -fix_mtl" but that did the opposite
>> of
>> what we need (i.e., it withdrew the pial surface so that it included none
>> of
>> the amygdala or hippocampus).
>>  much appreciated,
>> -David
>>
>> P.S. Thanks for creating and maintaining such an amazing suite of
>> freeware.
>>
>>
>>
>
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
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Re: [Freesurfer] mri_convert segfault error

[dgw]

If you must use 5.1 (I would recommend upgrading), then try what Zeke
suggested there.

You beat me to the email ;)

hth
d


On Thu, Jun 2, 2016 at 3:41 PM, Joshua Lee  wrote:
> Perhaps something to do with
>
> libcrypt-2.*.so ??
>
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040528.html
>
> -
> Joshua Lee, Ph.D.
> Post-Doctoral Researcher
> MIND Institute
> University of California, Davis
> 530.747.3805
>
> On Thu, Jun 2, 2016 at 12:36 PM, Joshua Lee  wrote:
>>
>> I do note that I can enter "freeview ./brain.mgz" and the image opens.
>> Then I can manuall save it as a .nii
>>
>> -
>> Joshua Lee, Ph.D.
>> Post-Doctoral Researcher
>> MIND Institute
>> University of California, Davis
>> 530.747.3805
>>
>> On Thu, Jun 2, 2016 at 12:33 PM, Joshua Lee  wrote:
>>>
>>> I had replaced the user name in the output I posted to the listserv for
>>> security reasons. I am not on a virtual machine. Fresh install on bare
>>> metal.
>>> ls -l ../
>>>
>>>> ...
>>>> drwxr-xr-x 13 myuser myuser  4096 Jun  2 11:50 mri
>>>> ...
>>>>
>>>
>>> -
>>> Joshua Lee, Ph.D.
>>> Post-Doctoral Researcher
>>> MIND Institute
>>> University of California, Davis
>>> 530.747.3805
>>>
>>> On Thu, Jun 2, 2016 at 12:25 PM, dgw  wrote:
>>>>
>>>> Is this a virtual machine? (The username seems odd...)
>>>>
>>>> What is the output of whoami?
>>>>
>>>> What is the output of ls -l ../?
>>>>
>>>> hth
>>>> d
>>>>
>>>>
>>>>
>>>> On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee  wrote:
>>>> > Hi Doug,
>>>> >
>>>> > Yes the quoted lines were output fromt her terminal.
>>>> >
>>>> >> ls -l brain.mgz
>>>> >> -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
>>>> >
>>>> >
>>>> > I have many Tb of disk space. I can chmod 777 the files and still seg
>>>> > faults.
>>>> >
>>>> > Thanks
>>>> > Josh
>>>> >
>>>> >
>>>> >
>>>> > -
>>>> > Joshua Lee, Ph.D.
>>>> > Post-Doctoral Researcher
>>>> > MIND Institute
>>>> > University of California, Davis
>>>> > 530.747.3805
>>>> >
>>>> > On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve
>>>> > 
>>>> > wrote:
>>>> >>
>>>> >> Can you send the full terminal output? Or is that it? Do you have
>>>> >> enough
>>>> >> disc space or is it running out? what is the result of
>>>> >> ls -l brain.mgz
>>>> >>
>>>> >>
>>>> >>
>>>> >> On 06/02/2016 03:07 PM, Joshua Lee wrote:
>>>> >> > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on
>>>> >> > Ubuntu 16.04 LTS
>>>> >> > mri_convert is seg faulting
>>>> >> >
>>>> >> >
>>>> >> > >>ls brain*
>>>> >> > brain.finalsurfs.mgz brainmask.auto.mgz  brainmask.mgz
>>>> >> > brain.mgz
>>>> >> >
>>>> >> > mri_convert ./brain.mgz --in_type mgz --out_type nii -o
>>>> >> > ./brain.nii
>>>> >> >
>>>> >> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>>>> >> > reading from ./brain.mgz...
>>>> >> > Segmentation fault (core dumped)
>>>> >> >
>>>> >> >
>>>> >> > Any ideas?
>>>> >> >
>>>> >> > Thanks
>>>> >> >
>>>> >> > Joshua
>>>> >> >
>>>> >> >
>>>> >> >
>>>> >> > ___
>>>> >> > Freesurfer mailing list
>>>> >> > Freesurfer@nmr.mgh.harvard.edu
>>>> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>> >>
>>>> >> --
>>>> >> Douglas N. Greve, Ph.D.
>>>> >> MGH-NMR Center
>>>> >

Re: [Freesurfer] mri_convert segfault error

[dgw]

Is this a virtual machine? (The username seems odd...)

What is the output of whoami?

What is the output of ls -l ../?

hth
d



On Thu, Jun 2, 2016 at 3:19 PM, Joshua Lee  wrote:
> Hi Doug,
>
> Yes the quoted lines were output fromt her terminal.
>
>> ls -l brain.mgz
>> -rwxrwx--- 1 myuser myuser 1216430 May 18 17:06 brain.mgz
>
>
> I have many Tb of disk space. I can chmod 777 the files and still seg
> faults.
>
> Thanks
> Josh
>
>
>
> -
> Joshua Lee, Ph.D.
> Post-Doctoral Researcher
> MIND Institute
> University of California, Davis
> 530.747.3805
>
> On Thu, Jun 2, 2016 at 12:13 PM, Douglas N Greve 
> wrote:
>>
>> Can you send the full terminal output? Or is that it? Do you have enough
>> disc space or is it running out? what is the result of
>> ls -l brain.mgz
>>
>>
>>
>> On 06/02/2016 03:07 PM, Joshua Lee wrote:
>> > On freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 installed on
>> > Ubuntu 16.04 LTS
>> > mri_convert is seg faulting
>> >
>> >
>> > >>ls brain*
>> > brain.finalsurfs.mgz brainmask.auto.mgz  brainmask.mgz  brain.mgz
>> >
>> > mri_convert ./brain.mgz --in_type mgz --out_type nii -o ./brain.nii
>> >
>> > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>> > reading from ./brain.mgz...
>> > Segmentation fault (core dumped)
>> >
>> >
>> > Any ideas?
>> >
>> > Thanks
>> >
>> > Joshua
>> >
>> >
>> >
>> > ___
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you in
>> error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>
>
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>
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> contains patient information, please contact the Partners Compliance
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Re: [Freesurfer] Customized ColorLUT - opacity value that will make regions totally transparent?

[dgw]

Hi Stephanie,

I think you will need to use the dev version of Freeview for the
"alpha" value to work properly.

hth
d

On Thu, May 5, 2016 at 12:08 PM, DeCross, Stephanie N.
 wrote:
> Hi all,
>
> I’m trying to open a couple aseg.mgz labels and color code them. I thought
> I’d do this by making my own ColorLUT table, setting the color of my
> regions, and then making every other region in the table be completely
> transparent by fiddling with the opacity value. I can’t figure out what
> number I want in the opacity column to make a region totally transparent,
> and on the wiki it says something about “255-alpha” for that column, but I
> don’t know what that means. In the opacity column I’ve tried values 0, 1,
> and 255, and it all looks the same (completely opaque) - anyone know what
> value I want there?
>
> Attached is my ColorLUT table, which currently gives me yellow caudate and
> green amyg and hippo (what I want), and the rest of the aseg.mgz labels are
> all black (I’m trying to change all the black to 100% transparent so they
> don’t show up at all and all I see are my yellow and green regions).
> Thanks!!
>
> (If it’s relevant, I’m loading the fsaverage orig.mgz and aseg.mgz into
> freeview and loading my ColorLUT table onto the aseg.mgz there, because I
> can’t figure out how to get this working in tkmedit).
>
> Best,
> Stephanie
>
> Stephanie N. DeCross
> Clinical Research Coordinator
> Psychiatric Neuroimaging Research Program
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street, Rm 2620A
> Charlestown, MA 02129
> Phone: (617) 724-3283
> Fax: (617) 726-4078
>
>
>
>
>
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Re: [Freesurfer] Preprocessing functional MRI

[dgw]

Martin,

You need to provide more details for us to help you. What version of
FreeSurfer? What exactly did you type in the command line as both your
analysis and your call to freeview?

If I were to take a wild guess, I would say you have the wrong surface
loaded. That tutorial does the analysis on the fsaverage inflated
surface.

hth
d

On Tue, Apr 26, 2016 at 4:07 PM, Martin Juneja  wrote:
> Hello again,
>
> Somehow I figured out the error I had related to *.config. Now I am able to
> run successfully all the 8 steps for 1 subject. I can see all the files
> generated in a new folder i.e. ces.nii.gz, cesvar.nii.gz, sig.nii.gz etc.
> But when I try to display any of these files using FreeView (after
> overlaying over inflated surface), it doesn't display anything and gives me
> error "freadFloat: fread failed".
>
> I would really appreciate any suggestions how can I display functional
> connectivity maps?
>
> Thanks,
> MJ
>
> On Tue, Apr 26, 2016 at 10:53 AM, Martin Juneja  wrote:
>>
>> Hello everyone,
>>
>> I am following this page to process fMRI data:
>>
>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough
>>
>> I am able to run until step-3 but at step 4, I am not sure what should be
>> directory to run this command. If I run the command in SUBJECTS_DIR
>> directory, it runs for a second and creates a mean*.config file. But next
>> step 5 requires *.config file to run, not the mean*.config
>>
>> Just a quick background:
>> I preprocessed all subjects structural data using recon-all and the
>> processed folders are in my FreeSurfer SUBJECTS_DIR path and the folder
>> after preprocessing functional data (after running step-3) is also in
>> SUBJECTS_DIR path.
>>
>> Any help would be greatly appreciated.
>>
>> MJ
>
>
>
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Re: [Freesurfer] white matter edits not incorporated

[dgw]

Hi,

I solved it (with help from a colleague) by just calling the
individual mri_make_surfaces command separately (adjusting the
nowhite), and
the subsequent ones through the flair pial command. I am now running
-make all, to finish the rest (note it did miss one step in the
re-start: it didn't re-run mris_calc, for bug hunting purposes), I
will re-run after it finishes.

Thanks everyone!
d

On Thu, Apr 21, 2016 at 4:55 PM, Bruce Fischl
 wrote:
> Hi Mike
>
> yes, I think it is fixed. Daniel: can you try out dev and see if it fixes
> this for you?
> Bruce
>
>
>
>
> On Thu, 21 Apr 2016, Harms, Michael wrote:
>
>>
>> That looks very similar in principle to something I posted back in Oct.
>> 2014 (“pial surface crossing white”).
>>
>> I think some of the subsequent back-and-forth with Bruce and Nick was off
>> the list, so I’ve included the key email (where Bruce diagnosed the
>> problem) below.
>>
>> Has this been fixed in the forthcoming FS 6.0?
>>
>> thanks,
>> -MH
>>
>>  snip 
>>
>> ok, I see what's going on. Here is the sequence of calls:
>>
>> 1. mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs
>> L408_base lh
>>
>> Makes the white surface *without* using the aparc. Because there are a
>> string of "hypointensity" labels in the aseg, the white surface is frozen
>> in these locations.
>>
>> 2.  mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs L408_base
>> lh
>>
>> internally recreates the white surface but doesn't save it. The frozen
>> vertices are allowed to move since the aparc *is* used in this call, and
>> the vertices are deemed to be in real cortical regions.
>>
>> The pial surface then starts from the (inwards deformed but not written to
>> disk) white surface, and then settles inside the white surface that is on
>> disk.
>>
>> I'm not sure how we settled on this logic. Why recreate the white surface?
>> Why not run with -nowhite -orig_pial white? That way the algorithm uses
>> the
>> white surface that the user can see and things should be consistent
>>
>> Bruce
>>
>>  end-snip 
>>
>>
>>
>> --
>> Michael Harms, Ph.D.
>>
>> -------
>> Conte Center for the Neuroscience of Mental Disorders
>> Washington University School of Medicine
>> Department of Psychiatry, Box 8134
>> 660 South Euclid Ave.Tel: 314-747-6173
>> St. Louis, MO  63110Email: mha...@wustl.edu
>>
>>
>>
>>
>> On 4/21/16, 9:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
>> dgw" > dgwake...@gmail.com> wrote:
>>
>> Hi,
>>
>> I followed the advice, and the White Matter surface looks much better;
>> however, now the pial surface is crossing the white matter surface.
>>
>> I ran the following:
>> /usr/local/freesurfer/stable5_3_0/bin/recon-all
>> -subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8
>>
>> for those at Martinos the new subjid should indicate the new path.
>>
>> I've attached a screenshot. Thank you in advance for any advice you can
>> give.
>>
>> Thank You,
>> Dan
>>
>> On Tue, Apr 19, 2016 at 5:29 PM, dgw  wrote:
>>>
>>> Hi Bruce,
>>>
>>> Thanks! I'll give it a whirl.
>>>
>>> d
>>>
>>> On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
>>>  wrote:
>>>>
>>>> Hi Daniel
>>>>
>>>> the problems isn't that it it's ignoring the wm edits, it is that it
>>>> starts
>>>> the orig surface out there, but then retracts to the (same) visible
>>>> gray/white boundary that it found in the first place. For this type of
>>>> lesion I think what you should do is also edit those voxels in the
>>>> aseg.mgz
>>>> and change them to right-lesion. This should freeze the white surface
>>>> there
>>>> I think. If it doesn't, let me know and I'll fix it.
>>>>
>>>> cheers
>>>> Bruce
>>>>
>>>>
>>>> On Tue, 19 Apr 2016, dgw wrote:
>>>>
>>>>> Here is the log for the most recent -autorecon2-wm call:
>>>>>
>>>>> Thanks!
>>>>> d
>>>>>
>>>>> On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
>>>>>  wrote:
>>>>>>
>>>>>> can you send us the 

Re: [Freesurfer] white matter edits not incorporated

[dgw]

Hi,

I followed the advice, and the White Matter surface looks much better;
however, now the pial surface is crossing the white matter surface.

I ran the following:
/usr/local/freesurfer/stable5_3_0/bin/recon-all
-subjid nmr01002 -autorecon2-wm -autorecon3 -openmp 8

for those at Martinos the new subjid should indicate the new path.

I've attached a screenshot. Thank you in advance for any advice you can give.

Thank You,
Dan

On Tue, Apr 19, 2016 at 5:29 PM, dgw  wrote:
> Hi Bruce,
>
> Thanks! I'll give it a whirl.
>
> d
>
> On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
>  wrote:
>> Hi Daniel
>>
>> the problems isn't that it it's ignoring the wm edits, it is that it starts
>> the orig surface out there, but then retracts to the (same) visible
>> gray/white boundary that it found in the first place. For this type of
>> lesion I think what you should do is also edit those voxels in the aseg.mgz
>> and change them to right-lesion. This should freeze the white surface there
>> I think. If it doesn't, let me know and I'll fix it.
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 19 Apr 2016, dgw wrote:
>>
>>> Here is the log for the most recent -autorecon2-wm call:
>>>
>>> Thanks!
>>> d
>>>
>>> On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
>>>  wrote:
>>>> can you send us the recon-all.log? I don't see an obvious reason why it
>>>> wouldn't have worked
>>>> On Tue, 19 Apr 2016, dgw wrote:
>>>>
>>>>> Just to follow up, I have tried several different options with
>>>>> recon-all to get the white matter edits to stick on this participant,
>>>>> and it doesn't seem to be working:
>>>>>
>>>>> re-editing wm.mgz and running recon-all -autorecon2-wm
>>>>> re-editing wm.mgz and running recon-all -make all
>>>>>
>>>>> I can't seem to get any appreciable change in the white matter
>>>>> surface. I have attached a screenshot, for an example.
>>>>>
>>>>> hth
>>>>> d
>>>>>
>>>>>
>>>>> On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I recently edited a brain with a gyral cyst, carefully filling the
>>>>>> cyst with white matter in the wm.mgz. Unfortunately after running:
>>>>>> /usr/local/freesurfer/stable5_3_0/bin/recon-all
>>>>>> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
>>>>>>
>>>>>> none of the edits were incorporated.
>>>>>>
>>>>>> Is the FLAIRpial flag incompatible with autorecon2-wm?
>>>>>>
>>>>>> Is there some other misake?
>>>>>>
>>>>>> I followed this guide
>>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview
>>>>>>
>>>>>> Thanks,
>>>>>> Dan
>>>>>
>>>> ___
>>>> Freesurfer mailing list
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>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to whom it 
>>>> is
>>>> addressed. If you believe this e-mail was sent to you in error and the 
>>>> e-mail
>>>> contains patient information, please contact the Partners Compliance 
>>>> HelpLine at
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>>>> error
>>>> but does not contain patient information, please contact the sender and 
>>>> properly
>>>> dispose of the e-mail.
>>>>
>>>
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Re: [Freesurfer] how to add skull and scalp and how to convert RAS coordinates

[dgw]

Hi Chiara,

look at the -surf option and the  -useSRAS option


We often use multi-echo FLASH/ PD images for generating these
surfaces, because standard MPRAGE type sequences lack contrast for
bone, see figure 17 here:
http://www.nmr.mgh.harvard.edu/~fischl/reprints/Neuroimage_Segonne_watershed.pdf

hth
d

On Wed, Apr 20, 2016 at 10:44 AM, Chiara Bulgarelli
 wrote:
> Many thanks Dr. Fischl for your support.
>
> My goal is to create a mesh completed of skull and scalp to be able to
> perform the Monte Carlo simulation on it.
> To do it, I need to start from a well segmented brain, so I decided to go
> for FreeSurfer.
>
> I have read something about the mri_watershed, but I could’t find any
> specific information about how exactly use it (my apologise, but I am quite
> new among the FreeSurfer users).
> Why do I need the T2 image to use this function?
>
> Many thanks in advance
>
> Best
>
> Chiara
>
>
>
> 
> Chiara Bulgarelli
> PhD Student, Centre for Brain and Cognitive Development
> Birkbeck College, University of London
>
> cbulg...@mail.bbk.ac.uk // bulgarelli.chia...@gmail.com
>
>
>
>
>
>
> On 20 Apr 2016, at 14:30, Bruce Fischl  wrote:
>
> Hi Chiara
>
> you can look at the mri_watershed help to see how to generate other tissue
> classes or boundary models, but typically you need some other image
> contrast(s) like T2/PD. What are you trying to accomplish?
>
> As for your second question, you should be able to use mri_surf2surf with
> the talairach.xfm to convert the surfaces to MNI coords, or just map to
> fsaverage which I believe is already in MNI space.
>
> cheers
> Bruce
>
> On Wed, 20 Apr 2016, Chiara Bulgarelli wrote:
>
> Dear FreeSurfer users, I am a PhD student from Birkbeck University and I am
> trying to segment some structural images of infants data.
> After the classical segmentation done with the ‘-recon all’ function, I am
> stuck with two issues:
> 1. How can I add the CSF, the skull and the scalp in my model? I know that
> with FS you can get just WM and GM.
> 2. How can I convert the RAS coordinates to MNI ones?
> I have been trying to look at these topics on line and on the FreeSurfer
> website, but I haven’t find anything useful so far.
> Many thanks in advance for your help!
> Best Regards
> Chiara
> 
> Chiara Bulgarelli
> PhD Student, Centre for Brain and Cognitive Development
> Birkbeck College, University of London
> cbulg...@mail.bbk.ac.uk // bulgarelli.chia...@gmail.com
>
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Re: [Freesurfer] white matter edits not incorporated

[dgw]

Hi Bruce,

Thanks! I'll give it a whirl.

d

On Tue, Apr 19, 2016 at 5:24 PM, Bruce Fischl
 wrote:
> Hi Daniel
>
> the problems isn't that it it's ignoring the wm edits, it is that it starts
> the orig surface out there, but then retracts to the (same) visible
> gray/white boundary that it found in the first place. For this type of
> lesion I think what you should do is also edit those voxels in the aseg.mgz
> and change them to right-lesion. This should freeze the white surface there
> I think. If it doesn't, let me know and I'll fix it.
>
> cheers
> Bruce
>
>
> On Tue, 19 Apr 2016, dgw wrote:
>
>> Here is the log for the most recent -autorecon2-wm call:
>>
>> Thanks!
>> d
>>
>> On Tue, Apr 19, 2016 at 4:56 PM, Bruce Fischl
>>  wrote:
>>> can you send us the recon-all.log? I don't see an obvious reason why it
>>> wouldn't have worked
>>> On Tue, 19 Apr 2016, dgw wrote:
>>>
>>>> Just to follow up, I have tried several different options with
>>>> recon-all to get the white matter edits to stick on this participant,
>>>> and it doesn't seem to be working:
>>>>
>>>> re-editing wm.mgz and running recon-all -autorecon2-wm
>>>> re-editing wm.mgz and running recon-all -make all
>>>>
>>>> I can't seem to get any appreciable change in the white matter
>>>> surface. I have attached a screenshot, for an example.
>>>>
>>>> hth
>>>> d
>>>>
>>>>
>>>> On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:
>>>>> Hi,
>>>>>
>>>>> I recently edited a brain with a gyral cyst, carefully filling the
>>>>> cyst with white matter in the wm.mgz. Unfortunately after running:
>>>>> /usr/local/freesurfer/stable5_3_0/bin/recon-all
>>>>> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
>>>>>
>>>>> none of the edits were incorporated.
>>>>>
>>>>> Is the FLAIRpial flag incompatible with autorecon2-wm?
>>>>>
>>>>> Is there some other misake?
>>>>>
>>>>> I followed this guide
>>>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview
>>>>>
>>>>> Thanks,
>>>>> Dan
>>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
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>>
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Re: [Freesurfer] white matter edits not incorporated

[dgw]

Just to follow up, I have tried several different options with
recon-all to get the white matter edits to stick on this participant,
and it doesn't seem to be working:

re-editing wm.mgz and running recon-all -autorecon2-wm
re-editing wm.mgz and running recon-all -make all

I can't seem to get any appreciable change in the white matter
surface. I have attached a screenshot, for an example.

hth
d


On Mon, Apr 18, 2016 at 10:30 AM, dgw  wrote:
> Hi,
>
> I recently edited a brain with a gyral cyst, carefully filling the
> cyst with white matter in the wm.mgz. Unfortunately after running:
> /usr/local/freesurfer/stable5_3_0/bin/recon-all
> -autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8
>
> none of the edits were incorporated.
>
> Is the FLAIRpial flag incompatible with autorecon2-wm?
>
> Is there some other misake?
>
> I followed this guide
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview
>
> Thanks,
> Dan
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Re: [Freesurfer] How to find the information from MRI data file

[dgw]

The nifti format is bad, and lacks that data, this will only work on
mgz files or dicoms.

hth
d

On Mon, Apr 18, 2016 at 11:54 AM, Mahmoud  wrote:
> Hi Bruce,
>
> I just ran it out of curiosity on T1w 3D-MPRAGE images from a Siemens
> scanner which has been converted to nifti using dcm2nii and I got this:
>
>  TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
>
> Which doesn't look correct? any comments?
>
> Thanks,
> Mahmoud
>
> On Mon, Apr 18, 2016 at 11:38 AM, Bruce Fischl 
> wrote:
>>
>> use mri_info
>>
>> cheers
>> Bruce
>>
>> On Mon, 18 Apr 2016, Muhammad Naveed Iqbal Qureshi wrote:
>>
>>>
>>> Hi,
>>>
>>> How can I find the following information from the MRI volume data already
>>> preprocessed with Freesurfer.
>>>
>>>
>>>
>>> 1.   Echo time
>>>
>>> 2.   Repetition time
>>>
>>> 3.   Flip angle
>>>
>>> Thank you.
>>>
>>>
>>>
>>> Best Regards,
>>> Muhammad Naveed Iqbal Qureshi
>>>
>>> P please don't print this e-mail unless you really need to
>>>
>>>
>>>
>>>
>>
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>
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[Freesurfer] white matter edits not incorporated

[dgw]

Hi,

I recently edited a brain with a gyral cyst, carefully filling the
cyst with white matter in the wm.mgz. Unfortunately after running:
/usr/local/freesurfer/stable5_3_0/bin/recon-all
-autorecon2-wm -autorecon3 -subjid nmr01002 -FLAIRpial -openmp 8

none of the edits were incorporated.

Is the FLAIRpial flag incompatible with autorecon2-wm?

Is there some other misake?

I followed this guide
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview

Thanks,
Dan
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Re: [Freesurfer] Installation issue

[dgw]

Try following the mac os install directions.

On Tue, Apr 5, 2016 at 1:57 PM,   wrote:
> Hi list,
>
> I'm reinstalling FS on my PC (iMac end of 2012).
> This error occur:
>
> freeview
>
> /Applications/freesurfer/bin/freeview.bin: Exec format error. Binary file
> not executable.
>
>
>
> Please take in account:
>
> freesurfer &   [1] 1818
>
> [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano%
>
> FreeSurfer is a set of tools for analysis and visualization
>
> of structural and functional brain imaging data. FreeSurfer
>
> also refers to the structural imaging stream within the
>
> FreeSurfer suite.
>
>
> Users should consult the online documentation available at:
>
>
>   https://surfer.nmr.mgh.harvard.edu
>
>
> Alternatively, the 'recon-all' command help-text provides
>
> adequate information to begin processing subject data, such
>
> as the sample subject 'bert' found in the 'freesurfer/subjects'
>
> directory.  Type 'recon-all --help' to view this help-text.
>
>
> Direct comments and questions to:
>
>
>   freesurfer@nmr.mgh.harvard.edu
>
>
> You are running this version of FreeSurfer:
>
>
>   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>
>
>
> Thanks
>
>
> Stefano
>
>
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Re: [Freesurfer] Visualising regional values on the surface

[dgw]

Hi Kirstie,

You could write your own CLUT file with the color corresponding to the
correlation you want to show?
Just open up the file and play with the values in the color columns.
Then simply load the color table in Freeview and use it to visualize
the annotation.

There are of course other ways, but this is probably the quickest.

hth
d


On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker  wrote:
> Hi,
>
> I'd like to show correlation coefficients by region on the brain surface. So
> for example, if I've calculated a modular decomposition in a network
> analysis for each region of the D-K atlas I'd like to be able to color each
> atlas region according to the module it has been assigned to.
>
> It seems like I have to do something with the ?h.aparc.annot files and a
> colour lookup table but I'm not sure exactly what.
>
> Thank you!
> Kx
>
> --
> Kirstie Whitaker, PhD
> Research Associate
>
> Department of Psychiatry
> University of Cambridge
>
> Mailing Address
> Brain Mapping Unit
> Department of Psychiatry
> Sir William Hardy Building
> Downing Street
> Cambridge CB2 3EB
>
> Phone: +44 7583 535 307
> Website: www.kirstiewhitaker.com
>
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Re: [Freesurfer] Mismatch in dimensions using mri_label2vol

[dgw]

I'll take a stab.

On Mon, Mar 28, 2016 at 10:13 AM, Afzal, Afsana  wrote:
> Hi, Just wanted to follow up on the issue below regarding the dimension of
> the mri_label2vol output.
>
>
> Hi,
>
> I'm using mri_label2vol with the parameters below but the output .nii volume
> has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension
> mismatch is causing issues in our gPPI pipeline.
>
> How can I generate a .nii output file with the 27307x1x6 dimension?

I don't think that is what you want. That NIFTI has the following
dimensions: vertices, N/A, timepoints.

It doesn't make sense to make a nifti label file (typically a volume)
out of surface data.

What volume are you using in your gPPI pipeline?
You will probably want a 3d volume nifti file not one with surface data in it.

hth
d

>
> mri_label2vol
> --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from
> preproc step)
> --label label_name.label
> --o label_name.nii
> --identity
>
> Thanks,
>
> Afsana
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Afzal, Afsana
> [aaf...@mgh.harvard.edu]
> Sent: Wednesday, March 23, 2016 2:44 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Mismatch in dimensions using mri_label2vol
>
> Hi,
>
> I'm using mri_label2vol with the parameters below but the output .nii volume
> has the shape 163842x1x1 while the input volume is 27307x1x6. This dimension
> mismatch is causing issues in our gPPI pipeline.
>
> How can I generate a .nii output file with the 27307x1x6 dimension?
>
> mri_label2vol
> --temp fmcpr.sm4.fsaverage.lh.b0dc.nii (output file generated from
> preproc step)
> --label label_name.label
> --o label_name.nii
> --identity
>
> Thanks,
>
> Afsana
>
> __
> Afsana Afzal
> Clinical Research Coordinator
> Massachusetts General Hospital
> Division of Neurotherapeutics
> Department of Psychiatry: Neurosciences
> 149 13th St, Room 2612
> Charlestown, MA 02129
> Phone: 617-643-5129
> Fax: 617-726-4078
>
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Re: [Freesurfer] Is it possible to use the mris_make_face_parcellation with the ico6 mesh?

[dgw]

first caveat, I could be wrong:

On Fri, Mar 25, 2016 at 3:18 PM, Michael Waskom  wrote:
> Hi,
>
> Can you say a bit more about what you mean?
>
>> If my memory serves, as you go to higher resolutions you end up with
>> multiple points being mapped to the same location,
>
> Do you mean multiple icosahedron vertices being mapped to the same native
> mesh vertex, or the other way around?

I can't remember correctly, this is one of those cases, where I remember it was
surprising and confusing, but can't remember what the right answer was
>
> In any case, the issue here is a little bit different, in that it is just
> raised when trying to generate a color table for the annotation:
> https://github.com/neurodebian/freesurfer/blob/master/utils/colortab.c#L540

I'm wondering if that is just a quirk of the error reporting, because
the check for
multiple vertices in FreeSurfer is at the colortab stage.

hth
d
>
> Michael
>
> On Fri, Mar 25, 2016 at 11:27 AM, dgw  wrote:
>>
>> Hi Michael,
>>
>> I think this is a problem that crops up periodically for us in the
>> MEEG world, where we use these downsampling
>> as calculated in MNE. If my memory serves, as you go to higher
>> resolutions you end up with multiple points
>> being mapped to the same location, which I don't believe we have ever
>> found a solution to. Note, this can even happen
>> at ico 5 (particularly on smaller brains).
>>
>>
>> hth
>> d
>>
>> On Fri, Mar 25, 2016 at 2:20 PM, Michael Waskom 
>> wrote:
>> > Hi Freesurfers,
>> >
>> > I'd like to use mris_make_face_parcellation to downsample an individual
>> > subject's surface mesh to a resolution similar to fsaverage6.
>> >
>> > My understanding is that mris_make_face_parcellation should let me do
>> > this,
>> > and it does what I expect with ic3-5. However when I run it with ic6 as
>> > the
>> > target, it fails:
>> >
>> > [surf]$ mris_make_face_parcellation lh.sphere
>> > $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot
>> > Reading lh.sphere
>> > Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri
>> > parcellating hemisphere into 40962 units
>> > INFO: CTABunique() could not find a unique set in 10 tries
>> > INFO: CTABunique() could not find a unique set in 100 tries
>> > ERROR: could not find a unique color table
>> >
>> > I don't really care if the colors themselves are distinct, and it should
>> > be
>> > possible to just programmatically generate a valid color table (since
>> > 255 ^
>> > 3 > 40962). I thought that providing a colortable with unique values
>> > through
>> > the -ctab option might work, but looking at the source code it seems
>> > that
>> > option will *write* a colortable, not read one.
>> >
>> > So, is there any way to accomplish the downsampling I want?
>> >
>> > Thanks in advance,
>> > Michael
>> >
>> > ___
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>> >
>> >
>> > The information in this e-mail is intended only for the person to whom
>> > it is
>> > addressed. If you believe this e-mail was sent to you in error and the
>> > e-mail
>> > contains patient information, please contact the Partners Compliance
>> > HelpLine at
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>> > in
>> > error
>> > but does not contain patient information, please contact the sender and
>> > properly
>> > dispose of the e-mail.
>> >
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Re: [Freesurfer] Is it possible to use the mris_make_face_parcellation with the ico6 mesh?

[dgw]

Hi Michael,

I think this is a problem that crops up periodically for us in the
MEEG world, where we use these downsampling
as calculated in MNE. If my memory serves, as you go to higher
resolutions you end up with multiple points
being mapped to the same location, which I don't believe we have ever
found a solution to. Note, this can even happen
at ico 5 (particularly on smaller brains).


hth
d

On Fri, Mar 25, 2016 at 2:20 PM, Michael Waskom  wrote:
> Hi Freesurfers,
>
> I'd like to use mris_make_face_parcellation to downsample an individual
> subject's surface mesh to a resolution similar to fsaverage6.
>
> My understanding is that mris_make_face_parcellation should let me do this,
> and it does what I expect with ic3-5. However when I run it with ic6 as the
> target, it fails:
>
> [surf]$ mris_make_face_parcellation lh.sphere
> $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot
> Reading lh.sphere
> Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri
> parcellating hemisphere into 40962 units
> INFO: CTABunique() could not find a unique set in 10 tries
> INFO: CTABunique() could not find a unique set in 100 tries
> ERROR: could not find a unique color table
>
> I don't really care if the colors themselves are distinct, and it should be
> possible to just programmatically generate a valid color table (since 255 ^
> 3 > 40962). I thought that providing a colortable with unique values through
> the -ctab option might work, but looking at the source code it seems that
> option will *write* a colortable, not read one.
>
> So, is there any way to accomplish the downsampling I want?
>
> Thanks in advance,
> Michael
>
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Re: [Freesurfer] mri_robust_register question

[dgw]

Hi Ji-Won,

Why not just input both T1s to recon-all it will motion correct and
average and then all of your functionals will be registered to the
same FS data?

hth
d

On Thu, Mar 17, 2016 at 3:06 PM, Ji Won Bang  wrote:
> Dear. All.
>
> Hi. How are you?
>
> It might be a very naive question, but your advice is greatly appreciated!
>
> I'm trying to register 2 T1s obtained from 1 subject on different days and
> then register the functional scans to their corresponding T1s (registering
> the functional scans to the same day's T1). By doing so, I expect to get
> everything into the same space.
>
> (Each subject was scanned twice on two different days etc., day1 and day2)
>
> After running mri_robust_register onto day2's T1 as targetting day1's T1, I
> get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run
> preproc-sess(that does registration as well) onto day2's functional scans.
>
> Is there a way to make preproc-sess do register functional scans of day2 to
> v2to1.mgz(of day2 that's created by mri_robust_register), not the original
> 046.mgz?
>
> The commands that I run are:
>
> recon-all -s $SUBJECT -all
>
> mri_robust_register --mov
> /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst
> /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta
> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov
> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights
> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz --iscale
> --satit
>
> preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force
> -fwhm 0
>
> Please feel free to give me any advice!
>
> Thank you very much.
>
> Best,
> Ji Won
>
>
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Re: [Freesurfer] System crash by extremely much generated output v6 beta

[dgw]

Hi Ed,

I am a bit confused by your two emails.

In one you state that you have a
MacPro OSX10.7 installed on a partition of 20 GB with FreeSurfer v6 beta

Then in the next post you state that the disk you have is 1.5TB (is that 
the disk or partition?)

I'm also confused, because you stated that at the time you ran into 
trouble the disk had 11GB. You then said you ran out of disk (I assume 
that means you had 0GB left). Then you said when you rebooted you had 
11GB (no files were created at all?).

This is a dangerous way in general to run a machine. If a program core 
dumps you have less disk space then your RAM. General advice is to keep 
at least 5% of disk space free (or a bare minimum of > RAM size). It may 
be worth doing this after a fresh reboot and checking your RAM to make 
sure you don't have apps that autostart sucking up RAM, causing you to 
swap. If you try to swap, without enough free space that can easily 
crash your machine.

First, What is the full disk partition setup?

Next, run df (on the relevant partition) and show the output before 
running FreeSurfer.

Then run recon-all and if possible show the df output at the crash

Then run df on reboot.

hth
d

PS it may be worth pointing out that beta 6 was withdrawn for more 
development.

On 3/10/16 5:09 AM, Gronenschild Ed (NP) wrote:
> Hi,
>
> I'm using a MacPro with 32 GByte RAM.
> The output of FreeSurfer is written to a disk with 1.5 TByte free space.
>
> At the time I ran into trouble the free disk space was about 11 GByte.
> When I wanted to inspect the progress after a few hours I noticed
> that the disk has ran out of space. I couldn't do anything but restarting
> the MacPro. Then the disk space was again about 11 GByte.
> So I reran the subject with recon-all -autorecon2 -autorecon3 and
> it happened again. Inspecting the log files I noticed that both times
> the problem occurred at exactly the same stage in the pipeline:
> mris-topo-fixer.
>
> Cheers,
> Ed
>
> On 10 Mar 2016, at 10:41,  >
>   wrote:
>
>> 20 GB is not a lot for a full macos install + data, how much room was
>> free before you ran recon-all?
>> What is the hardware? CPU, RAM etc.
>>
>> hth
>> d
>>
>> On Wed, Mar 9, 2016 at 12:09 PM, Gronenschild Ed (NP)
>> > > wrote:
>>> Hi developers,
>>>
>>> Could you please help me out on this problem.
>>> Should I upload the data?
>>>
>>> Cheers,
>>> Ed
>>>
>>> Begin forwarded message:
>>>
>>> From: Ed Gronenschild >> >
>>> Subject: System crash by extremely much generated output v6 beta
>>> Date: 7 March 2016 12:57:57 CET
>>> To: >> >
>>>
>>> Hi developers,
>>>
>>> My environment:
>>> MacPro OSX10.7 installed on a partition of 20 GByte;
>>> FreeSurfer v6 beta
>>>
>>> During processing recon-all on 4 subjects in parallel
>>> using 4 terminal windows, the 20 GByte partition got
>>> full. This happened twice and I managed to trace down
>>> the offending stage in the pipeline: topology fixing,
>>> in particular the tool mris_topo_fixer.
>>> Most probably it went into an endless iteration loop
>>> generating so much output the disk got full.
>>>
>>> Cheers,
>>> Ed
>>
>
>
>
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>
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> at
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Re: [Freesurfer] System crash by extremely much generated output v6 beta-Repost

[dgw]

20 GB is not a lot for a full macos install + data, how much room was
free before you ran recon-all?
 What is the hardware? CPU, RAM etc.

hth
d

On Wed, Mar 9, 2016 at 12:09 PM, Gronenschild Ed (NP)
 wrote:
> Hi developers,
>
> Could you please help me out on this problem.
> Should I upload the data?
>
> Cheers,
> Ed
>
> Begin forwarded message:
>
> From: Ed Gronenschild 
> Subject: System crash by extremely much generated output v6 beta
> Date: 7 March 2016 12:57:57 CET
> To: 
>
> Hi developers,
>
> My environment:
> MacPro OSX10.7 installed on a partition of 20 GByte;
> FreeSurfer v6 beta
>
> During processing recon-all on 4 subjects in parallel
> using 4 terminal windows, the 20 GByte partition got
> full. This happened twice and I managed to trace down
> the offending stage in the pipeline: topology fixing,
> in particular the tool mris_topo_fixer.
> Most probably it went into an endless iteration loop
> generating so much output the disk got full.
>
> Cheers,
> Ed
>
>
>
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>
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> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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Re: [Freesurfer] Embed vol geom in surf file

[dgw]

Marmaduke,

Could you describe what it is you want to do? What do you mean by
volume geometry? What type of information do you want to put on the
surface?

d

On Mon, Mar 7, 2016 at 2:31 PM, marmaduke woodman
 wrote:
> hi
>
> Is it possible to embed a volume geometry in a surface file explicitly?
> I'm unable to find a mri_ or mris_ command which seems to do this. Is
> there any workaround via the GUI tools?
>
>
> Thanks,
> Marmaduke
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

just change the values and re-run with different numbers and see what happens

On Wed, Mar 2, 2016 at 2:59 PM, Faeze Vedaei  wrote:
> Hi,
>
> Thank you for your response. sorry, I could not understand what you mean.
> How you found 23 230 60 values for paracentral region? I mean. Are these
> from Freesurfer LUT?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 9:33 PM, Faeze Vedaei  wrote:
>>
>> Thank you for your response. It is better to explain my question that the
>> coordinates for paracentral in .ctab file is '63 100 60', that you changed
>> these to '23 230 60' in your new version. My question is that how you
>> applied such this change on the RBG values for this region?
>>
>> Regards,
>> Faezeh
>>
>> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Thank you so much for you response. I should say that I know about what
>>> you are saying. My issue is that I have these 4 columns in my LUT file. Why
>>> and how can I change the numbers (RGB values) to create new LUT?
>>>
>>> Bests,
>>> Faezeh
>>>
>>> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 Thank you so much for you descriptions. I checked out the link you just
 sent me. Because I do not have many experiences working with Freesurfer, I
 really could not understand about how I can do such this revising in LUT
 file. Can you explain more about this? I truly appreciate your time and
 help.

 Regards,
 Faezeh Vedaei

 On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei 
 wrote:
>
> Hi,
>
> I really appreciate you for help me in this process. May you clarify me
> from which pattern you changed the RGB values for that region? How I can
> change the coordinates for the others?
>
> Regards,
> Faezeh Vedaei
>
>
> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
> wrote:
>>
>> Hi,
>>
>> I should let you know that, it works! It shows paracentral name in
>> tksurfer. So, how I have to revise my .ctab file to get the right result?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> Thank you for your response. I just used the command you suggested to
>>> use by just a change in calling .ctab LUT file. I used the path:
>>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by 
>>> just
>>> calling aparc.annot.a2009s.ctab. It is strange that I created annot 
>>> file for
>>> lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
>>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
>>> opinion?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
>>> wrote:

 Hi,


 Here is the text format of those files.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei
  wrote:
>
> Hi
>
> Thank you so much for your response. I attached here three files
> including the command lines, LUT file , and the list of names I want 
> to get
> and what the result is actually. I'd appreciate if you look at them 
> and let
> me know what is wrong with that.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei
>  wrote:
>>
>> Hi,
>>
>> I checked again to arrange the labels in the order of LUT file,
>> but the result has not changed. Can you help me more how I can fix 
>> this
>> problem? Thank you so much for your time and help.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei
>>  wrote:
>>>
>>> Hi,
>>>
>>> Thank you for your response. Yes, you are right. The names come
>>> from the color LUT file. But, the issue is that I chose the label 
>>> files from
>>> that LUT file too. It meas the source that I chose the label files 
>>> from and
>>> the source of the region's names in tksurfer are the same. The 
>>> problem is
>>> just I do not have the label's names I merged to create annot file, 
>>> in the
>>> tksurfer GUI. It shows another names of that list! So, what do you 
>>> think
>>> about? What is the problem?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei
>>>  wrote:

 Hi Freesurfer experts,

 I have created an annotation file by several label files using
 mris_label2annot command in Freesurfer. The problem is that when I 
 

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Those numbers only refer to the color the too will appear: hence the name color 
lookup table
hth
d

Sent from my Phone

> On Mar 1, 2016, at 21:33, Faeze Vedaei  wrote:
> 
> Thank you for your response. It is better to explain my question that the 
> coordinates for paracentral in .ctab file is '63 100 60', that you changed 
> these to '23 230 60' in your new version. My question is that how you applied 
> such this change on the RBG values for this region?
> 
> Regards,
> Faezeh
> 
>> On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei  wrote:
>> Thank you so much for you response. I should say that I know about what you 
>> are saying. My issue is that I have these 4 columns in my LUT file. Why and 
>> how can I change the numbers (RGB values) to create new LUT?
>> 
>> Bests,
>> Faezeh
>> 
>>> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei  wrote:
>>> Hi,
>>> 
>>> Thank you so much for you descriptions. I checked out the link you just 
>>> sent me. Because I do not have many experiences working with Freesurfer, I 
>>> really could not understand about how I can do such this revising in LUT 
>>> file. Can you explain more about this? I truly appreciate your time and 
>>> help.
>>> 
>>> Regards,
>>> Faezeh Vedaei
>>> 
 On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei  wrote:
 Hi,
 
 I really appreciate you for help me in this process. May you clarify me 
 from which pattern you changed the RGB values for that region? How I can 
 change the coordinates for the others?
 
 Regards,
 Faezeh Vedaei
 
 
> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei  
> wrote:
> Hi,
> 
> I should let you know that, it works! It shows paracentral name in 
> tksurfer. So, how I have to revise my .ctab file to get the right result?
> 
> Regards,
> Faezeh Vedaei
> 
>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei  
>> wrote:
>> Hi,
>> 
>> Thank you for your response. I just used the command you suggested to 
>> use by just a change in calling .ctab LUT file. I used the path: 
>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by 
>> just calling aparc.annot.a2009s.ctab. It is strange that I created annot 
>> file for lh.G_and_S_paracentral.label, but it shows its name in 
>> tksurfer: G_and_S_frontomarg! I excluded the part --nhits too. So, what 
>> is your opinion?
>> 
>> Regards,
>> Faezeh Vedaei
>> 
>>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei  
>>> wrote:
>>> Hi,
>>> 
>>> 
>>> Here is the text format of those files.
>>> 
>>> Regards,
>>> Faezeh Vedaei
>>> 
 On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei  
 wrote:
 Hi
 
 Thank you so much for your response. I attached here three files 
 including the command lines, LUT file , and the list of names I want 
 to get and what the result is actually. I'd appreciate if you look at 
 them and let me know what is wrong with that. 
 
 Regards,
 Faezeh Vedaei
 
> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei  
> wrote:
> Hi,
> 
> I checked again to arrange the labels in the order of LUT file, but 
> the result has not changed. Can you help me more how I can fix this 
> problem? Thank you so much for your time and help.
> 
> Regards,
> Faezeh Vedaei
> 
>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>>  wrote:
>> Hi,
>> 
>> Thank you for your response. Yes, you are right. The names come from 
>> the color LUT file. But, the issue is that I chose the label files 
>> from that LUT file too. It meas the source that I chose the label 
>> files from and the source of the region's names in tksurfer are the 
>> same. The problem is just I do not have the label's names I merged 
>> to create annot file, in the tksurfer GUI. It shows another names of 
>> that list! So, what do you think about? What is the problem?
>> 
>> Regards,
>> Faezeh Vedaei
>> 
>>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
>>>  wrote:
>>> Hi Freesurfer experts,
>>> 
>>> I have created an annotation file by several label files using 
>>> mris_label2annot command in Freesurfer. The problem is that when I 
>>> open this annot file in tksurfer and click on colored regions which 
>>> corresponded to specific labels I had chosen them, I do not have 
>>> their name on the vertex information part at the bottom of tksurfer 
>>> GUI. It shows very different names for these regions. May you 
>>> explains me what is the problem I could not see the exact region's 
>>> name as I have them for label files?
>>> 
>>> Thanks,
>>> 

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

It is just a text file (you can open it with vi or gedit whatever),
just add new lines for new labels and make the colors the color you
want them to be.\

hth
d

On Tue, Mar 1, 2016 at 5:55 PM, Faeze Vedaei  wrote:
> Thank you so much for you response. I should say that I know about what you
> are saying. My issue is that I have these 4 columns in my LUT file. Why and
> how can I change the numbers (RGB values) to create new LUT?
>
> Bests,
> Faezeh
>
> On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> Thank you so much for you descriptions. I checked out the link you just
>> sent me. Because I do not have many experiences working with Freesurfer, I
>> really could not understand about how I can do such this revising in LUT
>> file. Can you explain more about this? I truly appreciate your time and
>> help.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> I really appreciate you for help me in this process. May you clarify me
>>> from which pattern you changed the RGB values for that region? How I can
>>> change the coordinates for the others?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>>
>>> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 I should let you know that, it works! It shows paracentral name in
 tksurfer. So, how I have to revise my .ctab file to get the right result?

 Regards,
 Faezeh Vedaei

 On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
 wrote:
>
> Hi,
>
> Thank you for your response. I just used the command you suggested to
> use by just a change in calling .ctab LUT file. I used the path:
> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
> calling aparc.annot.a2009s.ctab. It is strange that I created annot file 
> for
> lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
> opinion?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
> wrote:
>>
>> Hi,
>>
>>
>> Here is the text format of those files.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi
>>>
>>> Thank you so much for your response. I attached here three files
>>> including the command lines, LUT file , and the list of names I want to 
>>> get
>>> and what the result is actually. I'd appreciate if you look at them and 
>>> let
>>> me know what is wrong with that.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 I checked again to arrange the labels in the order of LUT file, but
 the result has not changed. Can you help me more how I can fix this 
 problem?
 Thank you so much for your time and help.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei
  wrote:
>
> Hi,
>
> Thank you for your response. Yes, you are right. The names come
> from the color LUT file. But, the issue is that I chose the label 
> files from
> that LUT file too. It meas the source that I chose the label files 
> from and
> the source of the region's names in tksurfer are the same. The 
> problem is
> just I do not have the label's names I merged to create annot file, 
> in the
> tksurfer GUI. It shows another names of that list! So, what do you 
> think
> about? What is the problem?
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei
>  wrote:
>>
>> Hi Freesurfer experts,
>>
>> I have created an annotation file by several label files using
>> mris_label2annot command in Freesurfer. The problem is that when I 
>> open this
>> annot file in tksurfer and click on colored regions which 
>> corresponded to
>> specific labels I had chosen them, I do not have their name on the 
>> vertex
>> information part at the bottom of tksurfer GUI. It shows very 
>> different
>> names for these regions. May you explains me what is the problem I 
>> could not
>> see the exact region's name as I have them for label files?
>>
>> Thanks,
>> Faezeh Vedaei
>
>

>>>
>>
>

>>>
>>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom i

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

The 4 number columns represent:
Red Green Blue and Alpha

The numbers range from 0-255. They can be combined to create any
color. Play around, and you will see what it does.

hth,
d

On Tue, Mar 1, 2016 at 5:37 PM, Faeze Vedaei  wrote:
> Hi,
>
> Thank you so much for you descriptions. I checked out the link you just sent
> me. Because I do not have many experiences working with Freesurfer, I really
> could not understand about how I can do such this revising in LUT file. Can
> you explain more about this? I truly appreciate your time and help.
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> I really appreciate you for help me in this process. May you clarify me
>> from which pattern you changed the RGB values for that region? How I can
>> change the coordinates for the others?
>>
>> Regards,
>> Faezeh Vedaei
>>
>>
>> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> I should let you know that, it works! It shows paracentral name in
>>> tksurfer. So, how I have to revise my .ctab file to get the right result?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 Thank you for your response. I just used the command you suggested to
 use by just a change in calling .ctab LUT file. I used the path:
 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
 calling aparc.annot.a2009s.ctab. It is strange that I created annot file 
 for
 lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
 G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
 opinion?

 Regards,
 Faezeh Vedaei

 On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
 wrote:
>
> Hi,
>
>
> Here is the text format of those files.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
> wrote:
>>
>> Hi
>>
>> Thank you so much for your response. I attached here three files
>> including the command lines, LUT file , and the list of names I want to 
>> get
>> and what the result is actually. I'd appreciate if you look at them and 
>> let
>> me know what is wrong with that.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> I checked again to arrange the labels in the order of LUT file, but
>>> the result has not changed. Can you help me more how I can fix this 
>>> problem?
>>> Thank you so much for your time and help.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 Thank you for your response. Yes, you are right. The names come from
 the color LUT file. But, the issue is that I chose the label files 
 from that
 LUT file too. It meas the source that I chose the label files from and 
 the
 source of the region's names in tksurfer are the same. The problem is 
 just I
 do not have the label's names I merged to create annot file, in the 
 tksurfer
 GUI. It shows another names of that list! So, what do you think about? 
 What
 is the problem?

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei
  wrote:
>
> Hi Freesurfer experts,
>
> I have created an annotation file by several label files using
> mris_label2annot command in Freesurfer. The problem is that when I 
> open this
> annot file in tksurfer and click on colored regions which 
> corresponded to
> specific labels I had chosen them, I do not have their name on the 
> vertex
> information part at the bottom of tksurfer GUI. It shows very 
> different
> names for these regions. May you explains me what is the problem I 
> could not
> see the exact region's name as I have them for label files?
>
> Thanks,
> Faezeh Vedaei


>>>
>>
>

>>>
>>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
___
Freesurfe

Re: [Freesurfer] mri_label2vol projfrac missing voxels

[dgw]

Hi,

I just wanted to post back the problem was solved (Thanks Doug). The
solution is this:

1. use mri_aparc2aseg
mri_aparc2aseg --s $SUBJECT --o .mgz --annot 
--annot-table 


[Note, in my case I was using 3 different values, 1, 2, 3 for the
labels with only left hemisphere labels (the details will change for
people with different label numbers etc.)]
2. read in the resulting file (python or matlab: pick your poison).
set all voxels less than 1001 to 0, set all voxels greater than 1003
to 0, remap voxels with value 1001 to 1, 1002 to 2 1003 to 3.

Now you are done and can load with your clut file.

hth
d

On Mon, Feb 29, 2016 at 2:16 PM, dgw  wrote:
> Hi,
>
> I just wanted to repost this question. After turning on the
> transparency, I also noticed that this problem goes both directions
> (i.e. some voxels which aren't gray matter in the lh.ribbon.mgz are
> labeled utilized when calling mri_label2vol.
>
> On Tue, Feb 23, 2016 at 3:19 PM, dgw  wrote:
>> Hi,
>>
>> I am having trouble with the projfrac option in mri_label2vol (on the
>> current dev freesurfer environment). When I use the following command:
>>
>> mri_label2vol --annot label/lh.lang.annot --subject nmr00937 --o
>> lang_seg.mgz --hemi lh --identity --temp mri/T1.mgz --proj frac 0 1
>> .01
>>
>> I get many missed voxels from the gray matter (see the attached image,
>> with the yellow representing the label overlaid on the ribbon.mgz). I
>> have tried more extreme delta values and this doesn't help. (note
>> scrolling to nearby slices indicates the neighboring voxels are
>> included, so it isn't from the angle projecting oddly (that is why I
>> took a slice from the middle of this large label)). Is there a better
>> way to convert the annotation to a volume just in the gray matter, but
>> including all of the relevant voxels?
>>
>> Is there a fundamental algorithmic difference between mris_volmask and
>> mri_label2vol?
>>
>> If yes, why?
>>
>> Thanks,
>> D
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faezeh,

Check this page out for details. The values are just numbers in the
columns of the file:

https://en.wikipedia.org/wiki/RGB_color_model

hth
d

On Tue, Mar 1, 2016 at 3:49 PM, Faeze Vedaei  wrote:
> Hi,
>
> I really appreciate you for help me in this process. May you clarify me from
> which pattern you changed the RGB values for that region? How I can change
> the coordinates for the others?
>
> Regards,
> Faezeh Vedaei
>
>
> On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> I should let you know that, it works! It shows paracentral name in
>> tksurfer. So, how I have to revise my .ctab file to get the right result?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> Thank you for your response. I just used the command you suggested to use
>>> by just a change in calling .ctab LUT file. I used the path:
>>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
>>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file for
>>> lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
>>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
>>> opinion?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
>>> wrote:

 Hi,


 Here is the text format of those files.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
 wrote:
>
> Hi
>
> Thank you so much for your response. I attached here three files
> including the command lines, LUT file , and the list of names I want to 
> get
> and what the result is actually. I'd appreciate if you look at them and 
> let
> me know what is wrong with that.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
> wrote:
>>
>> Hi,
>>
>> I checked again to arrange the labels in the order of LUT file, but
>> the result has not changed. Can you help me more how I can fix this 
>> problem?
>> Thank you so much for your time and help.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> Thank you for your response. Yes, you are right. The names come from
>>> the color LUT file. But, the issue is that I chose the label files from 
>>> that
>>> LUT file too. It meas the source that I chose the label files from and 
>>> the
>>> source of the region's names in tksurfer are the same. The problem is 
>>> just I
>>> do not have the label's names I merged to create annot file, in the 
>>> tksurfer
>>> GUI. It shows another names of that list! So, what do you think about? 
>>> What
>>> is the problem?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei
>>>  wrote:

 Hi Freesurfer experts,

 I have created an annotation file by several label files using
 mris_label2annot command in Freesurfer. The problem is that when I 
 open this
 annot file in tksurfer and click on colored regions which corresponded 
 to
 specific labels I had chosen them, I do not have their name on the 
 vertex
 information part at the bottom of tksurfer GUI. It shows very different
 names for these regions. May you explains me what is the problem I 
 could not
 see the exact region's name as I have them for label files?

 Thanks,
 Faezeh Vedaei
>>>
>>>
>>
>

>>>
>>
>
>
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

yes, just follow the pattern of the file. You will probably want to
use different RGB values to get different colored labels.

hth
d

On Tue, Mar 1, 2016 at 2:51 PM, Faeze Vedaei  wrote:
> Hi,
>
> I should let you know that, it works! It shows paracentral name in tksurfer.
> So, how I have to revise my .ctab file to get the right result?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> Thank you for your response. I just used the command you suggested to use
>> by just a change in calling .ctab LUT file. I used the path:
>> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
>> calling aparc.annot.a2009s.ctab. It is strange that I created annot file for
>> lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
>> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
>> opinion?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>>
>>> Here is the text format of those files.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
>>> wrote:

 Hi

 Thank you so much for your response. I attached here three files
 including the command lines, LUT file , and the list of names I want to get
 and what the result is actually. I'd appreciate if you look at them and let
 me know what is wrong with that.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
 wrote:
>
> Hi,
>
> I checked again to arrange the labels in the order of LUT file, but the
> result has not changed. Can you help me more how I can fix this problem?
> Thank you so much for your time and help.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
> wrote:
>>
>> Hi,
>>
>> Thank you for your response. Yes, you are right. The names come from
>> the color LUT file. But, the issue is that I chose the label files from 
>> that
>> LUT file too. It meas the source that I chose the label files from and 
>> the
>> source of the region's names in tksurfer are the same. The problem is 
>> just I
>> do not have the label's names I merged to create annot file, in the 
>> tksurfer
>> GUI. It shows another names of that list! So, what do you think about? 
>> What
>> is the problem?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi Freesurfer experts,
>>>
>>> I have created an annotation file by several label files using
>>> mris_label2annot command in Freesurfer. The problem is that when I open 
>>> this
>>> annot file in tksurfer and click on colored regions which corresponded 
>>> to
>>> specific labels I had chosen them, I do not have their name on the 
>>> vertex
>>> information part at the bottom of tksurfer GUI. It shows very different
>>> names for these regions. May you explains me what is the problem I 
>>> could not
>>> see the exact region's name as I have them for label files?
>>>
>>> Thanks,
>>> Faezeh Vedaei
>>
>>
>

>>>
>>
>
>
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faezeh,

Please run the exact commands including the file I attached, not the
aparc.annot.a2009s.ctab, and check the result using the freeview
command I provided. Then let me know what label freeview shows.

hth
d

On Tue, Mar 1, 2016 at 1:10 PM, Faeze Vedaei  wrote:
> Hi,
>
> Thank you for your response. I just used the command you suggested to use by
> just a change in calling .ctab LUT file. I used the path:
> 002_S_0413/labels/aparc.annot.a2009s.ctab because I could not work by just
> calling aparc.annot.a2009s.ctab. It is strange that I created annot file for
> lh.G_and_S_paracentral.label, but it shows its name in tksurfer:
> G_and_S_frontomarg! I excluded the part --nhits too. So, what is your
> opinion?
>
> Regards,
> Faezeh Vedaei
>
> On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>>
>> Here is the text format of those files.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi
>>>
>>> Thank you so much for your response. I attached here three files
>>> including the command lines, LUT file , and the list of names I want to get
>>> and what the result is actually. I'd appreciate if you look at them and let
>>> me know what is wrong with that.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 I checked again to arrange the labels in the order of LUT file, but the
 result has not changed. Can you help me more how I can fix this problem?
 Thank you so much for your time and help.

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
 wrote:
>
> Hi,
>
> Thank you for your response. Yes, you are right. The names come from
> the color LUT file. But, the issue is that I chose the label files from 
> that
> LUT file too. It meas the source that I chose the label files from and the
> source of the region's names in tksurfer are the same. The problem is 
> just I
> do not have the label's names I merged to create annot file, in the 
> tksurfer
> GUI. It shows another names of that list! So, what do you think about? 
> What
> is the problem?
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
> wrote:
>>
>> Hi Freesurfer experts,
>>
>> I have created an annotation file by several label files using
>> mris_label2annot command in Freesurfer. The problem is that when I open 
>> this
>> annot file in tksurfer and click on colored regions which corresponded to
>> specific labels I had chosen them, I do not have their name on the vertex
>> information part at the bottom of tksurfer GUI. It shows very different
>> names for these regions. May you explains me what is the problem I could 
>> not
>> see the exact region's name as I have them for label files?
>>
>> Thanks,
>> Faezeh Vedaei
>
>

>>>
>>
>
>
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>
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> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faezeh,

It is strange that the LUT file you sent doesn't seem to be named
anything similar to the file you called. You are calling

new/002_S_0413/labels/aparc.annot.a2009s.ctab

There also seem to be some basic issues with the command --s should
just have the name of the subject not a separate directory as well.

Why are you using the --nhits option?

Here is an example, of what I think is closer to what you want:

mris_label2annot --s 002_S_0413 --h lh --ctab faezeh_lut.ctab --a
myaparc_test --l 002_S_0413/labels/lh.G_and_S_paracentral.label

Work from there and see if that gets you the first one, then just add
as you go. Also check that you are properly loading the data in
freeview:

freeview -f 002_S_0413/surf/lh.inflated:annot=lh.myaparc_test.annot


hth
d

On Tue, Mar 1, 2016 at 10:57 AM, Faeze Vedaei  wrote:
> Hi,
>
>
> Here is the text format of those files.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei  wrote:
>>
>> Hi
>>
>> Thank you so much for your response. I attached here three files including
>> the command lines, LUT file , and the list of names I want to get and what
>> the result is actually. I'd appreciate if you look at them and let me know
>> what is wrong with that.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> I checked again to arrange the labels in the order of LUT file, but the
>>> result has not changed. Can you help me more how I can fix this problem?
>>> Thank you so much for your time and help.
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>>> wrote:

 Hi,

 Thank you for your response. Yes, you are right. The names come from the
 color LUT file. But, the issue is that I chose the label files from that 
 LUT
 file too. It meas the source that I chose the label files from and the
 source of the region's names in tksurfer are the same. The problem is just 
 I
 do not have the label's names I merged to create annot file, in the 
 tksurfer
 GUI. It shows another names of that list! So, what do you think about? What
 is the problem?

 Regards,
 Faezeh Vedaei

 On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
 wrote:
>
> Hi Freesurfer experts,
>
> I have created an annotation file by several label files using
> mris_label2annot command in Freesurfer. The problem is that when I open 
> this
> annot file in tksurfer and click on colored regions which corresponded to
> specific labels I had chosen them, I do not have their name on the vertex
> information part at the bottom of tksurfer GUI. It shows very different
> names for these regions. May you explains me what is the problem I could 
> not
> see the exact region's name as I have them for label files?
>
> Thanks,
> Faezeh Vedaei


>>>
>>
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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> dispose of the e-mail.
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faezeh_lut.ctab
Description: Binary data
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faezeh,

Can you send these in the text of the email. It is very hard to deal
with these files? The LUT file shouldn't be an excel file it should be
a plain text document (please attach).

Thanks,
D

On Mon, Feb 29, 2016 at 5:30 PM, Faeze Vedaei  wrote:
> Hi
>
> Thank you so much for your response. I attached here three files including
> the command lines, LUT file , and the list of names I want to get and what
> the result is actually. I'd appreciate if you look at them and let me know
> what is wrong with that.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> I checked again to arrange the labels in the order of LUT file, but the
>> result has not changed. Can you help me more how I can fix this problem?
>> Thank you so much for your time and help.
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi,
>>>
>>> Thank you for your response. Yes, you are right. The names come from the
>>> color LUT file. But, the issue is that I chose the label files from that LUT
>>> file too. It meas the source that I chose the label files from and the
>>> source of the region's names in tksurfer are the same. The problem is just I
>>> do not have the label's names I merged to create annot file, in the tksurfer
>>> GUI. It shows another names of that list! So, what do you think about? What
>>> is the problem?
>>>
>>> Regards,
>>> Faezeh Vedaei
>>>
>>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
>>> wrote:

 Hi Freesurfer experts,

 I have created an annotation file by several label files using
 mris_label2annot command in Freesurfer. The problem is that when I open 
 this
 annot file in tksurfer and click on colored regions which corresponded to
 specific labels I had chosen them, I do not have their name on the vertex
 information part at the bottom of tksurfer GUI. It shows very different
 names for these regions. May you explains me what is the problem I could 
 not
 see the exact region's name as I have them for label files?

 Thanks,
 Faezeh Vedaei
>>>
>>>
>>
>
>
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faezeh,

Please provide more details (those i described in the earlier email).

Thanks
d

On Mon, Feb 29, 2016 at 4:45 PM, Faeze Vedaei  wrote:
> Hi,
>
> I checked again to arrange the labels in the order of LUT file, but the
> result has not changed. Can you help me more how I can fix this problem?
> Thank you so much for your time and help.
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei  wrote:
>>
>> Hi,
>>
>> Thank you for your response. Yes, you are right. The names come from the
>> color LUT file. But, the issue is that I chose the label files from that LUT
>> file too. It meas the source that I chose the label files from and the
>> source of the region's names in tksurfer are the same. The problem is just I
>> do not have the label's names I merged to create annot file, in the tksurfer
>> GUI. It shows another names of that list! So, what do you think about? What
>> is the problem?
>>
>> Regards,
>> Faezeh Vedaei
>>
>> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
>> wrote:
>>>
>>> Hi Freesurfer experts,
>>>
>>> I have created an annotation file by several label files using
>>> mris_label2annot command in Freesurfer. The problem is that when I open this
>>> annot file in tksurfer and click on colored regions which corresponded to
>>> specific labels I had chosen them, I do not have their name on the vertex
>>> information part at the bottom of tksurfer GUI. It shows very different
>>> names for these regions. May you explains me what is the problem I could not
>>> see the exact region's name as I have them for label files?
>>>
>>> Thanks,
>>> Faezeh Vedaei
>>
>>
>
>
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faeze,

It is difficult to help without more details, but in my experience,
(exact command, the color lut file in text in the email and what the
error in the naming was, which label went to which entry in the color
lut.)

You need to put the labels in the order of your custom color lut file.

hth
d

On Mon, Feb 29, 2016 at 3:01 PM, Faeze Vedaei  wrote:
> Hi,
>
> Thank you for your response. Yes, you are right. The names come from the
> color LUT file. But, the issue is that I chose the label files from that LUT
> file too. It meas the source that I chose the label files from and the
> source of the region's names in tksurfer are the same. The problem is just I
> do not have the label's names I merged to create annot file, in the tksurfer
> GUI. It shows another names of that list! So, what do you think about? What
> is the problem?
>
> Regards,
> Faezeh Vedaei
>
> On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei 
> wrote:
>>
>> Hi Freesurfer experts,
>>
>> I have created an annotation file by several label files using
>> mris_label2annot command in Freesurfer. The problem is that when I open this
>> annot file in tksurfer and click on colored regions which corresponded to
>> specific labels I had chosen them, I do not have their name on the vertex
>> information part at the bottom of tksurfer GUI. It shows very different
>> names for these regions. May you explains me what is the problem I could not
>> see the exact region's name as I have them for label files?
>>
>> Thanks,
>> Faezeh Vedaei
>
>
>
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Re: [Freesurfer] The name of regions of annotation file issue viewing by tksurfer

[dgw]

Hi Faeze,

I believe the name comes from the Color LUT file. Try changing the
name in there.

hth
d

On Mon, Feb 29, 2016 at 12:42 PM, Faeze Vedaei  wrote:
> Hi Freesurfer experts,
>
> I have created an annotation file by several label files using
> mris_label2annot command in Freesurfer. The problem is that when I open this
> annot file in tksurfer and click on colored regions which corresponded to
> specific labels I had chosen them, I do not have their name on the vertex
> information part at the bottom of tksurfer GUI. It shows very different
> names for these regions. May you explains me what is the problem I could not
> see the exact region's name as I have them for label files?
>
> Thanks,
> Faezeh Vedaei
>
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Re: [Freesurfer] (no subject)

[dgw]

Maheen,

it sounds like a question that could be better answered by the Homer2 list.

hth
d

On Fri, Feb 26, 2016 at 8:13 AM, Maheen Siddiqui
 wrote:
> Dear FreeSurfer Users,
>
> I have a head surface mesh and a pial surface mesh obtained after
> segmentation of a T1 MRI scan. I am going to importing these into Homer2
> Atlas Viewer as subject anatomy.
>
> However before I can do this import successfully, I need to bring the two
> meshes into the same coordinate system. At the moment they are in different
> coordinate systems (as pictured) and I need to bring the pial surface mesh
> into the head surface mesh. I am a little unsure how to do this.
>
> Does anybody have any experience with this? Or any advice on what I could do
> possibly?
>
> Thanks,
>
> Maheen
>
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Re: [Freesurfer] Fwd: Creare Annot File in Freesurface

[dgw]

try specifying the full path to the label.

hth
d

On Wed, Feb 24, 2016 at 2:37 PM, Faeze Vedaei  wrote:
> Hil Freesurfer experts,
>
> I am trying to create annot file in freesurface using mris_label2annot
> command. In this process, I got an error : cannot find or read
> 'labelfile'sname.label'. I want to help me and explain what is the problem I
> have such this error for every label file I practice? Here is the command
> line I used :
>
> mris_label2annot --s 002_S_0295 --h lh --ctab
> 002_S_0295/LABELS/aparc.annot.a2009s.ctab --a myaparc --l lh.G_orbital.label
>
> ERROR: cannot find or read lh.G_orbital.label.
>
>
> I'd appreciate it if you clarify me about this process and how I can solve
> this.
>
> Regards,
> Faezeh Vedaei
>
>
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[Freesurfer] mri_label2vol projfrac missing voxels

[dgw]

Hi,

I am having trouble with the projfrac option in mri_label2vol (on the
current dev freesurfer environment). When I use the following command:

mri_label2vol --annot label/lh.lang.annot --subject nmr00937 --o
lang_seg.mgz --hemi lh --identity --temp mri/T1.mgz --proj frac 0 1
.01

I get many missed voxels from the gray matter (see the attached image,
with the yellow representing the label overlaid on the ribbon.mgz). I
have tried more extreme delta values and this doesn't help. (note
scrolling to nearby slices indicates the neighboring voxels are
included, so it isn't from the angle projecting oddly (that is why I
took a slice from the middle of this large label)). Is there a better
way to convert the annotation to a volume just in the gray matter, but
including all of the relevant voxels?

Is there a fundamental algorithmic difference between mris_volmask and
mri_label2vol?

If yes, why?

Thanks,
D
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Re: [Freesurfer] abnormal inflated surface

[dgw]

Hi Jasmin,

nothing looks wrong with the inflated brain images to me. Remember,
the inflated brain doesn't have the same space as the T1 or white
matter surface, so they are just centered. And overlap one another as
the slice views showed. I'm afraid I can't help with the hippocampal
question, though you may want to try adding some details.

hth
d

On Wed, Feb 10, 2016 at 5:30 PM, Jasmin Alves  wrote:
> Hello freesurfer,
>
> I received this odd inflated surface image. I am not sure if this is
> something that can be fixed via a registration step or should be fixed in
> another step. Your input as to how to correct this image would be greatly
> appreciated. Also, I noticed that this participant's hippocampal volume is
> half the amount compared to the rest of my participants. Is it possible
> these two problems are related or am I possibly dealing with two separate
> issues? I have attached a screen shot of both problems.
>
> Thank you very much,
> Jasmin
>
> --
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu
>
>
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Re: [Freesurfer] comparing multiple runs on the same scan

[dgw]

Doug responded to your previous mail with this:

Even on the same operating system they will be different because there
is stuff in the header that will change. Use mri_diff (volumes,
segmentations, and surface overlays) or mris_diff for surfaces to check
whether they are different.


hth
d


On Wed, Feb 10, 2016 at 2:14 PM, Krieger, Donald N. 
wrote:

> We would like to confirm that we are getting identical results from
> multiple freesurfer runs on the same data set.
>
> To do so we are comparing identically named files using md5sum and would
> very much appreciate your thoughts on our results.  For multiple files, we
> concatenate them and pipe the output into md5sum.  Below is a table showing
> what we’ve found so far.  I take hope from the positive matches we get from
> all of the .annot files and from the fact that 001.mgz does not match.
> This latter suggests that there is a date or something embedded in some of
> the files from separate runs which defeats the match.
>
>
>
> Please let us know what you know about this and thanks.
>
>
>
> file(s)
>
> md5sum result
>
> label/*.annot
>
> match
>
> label/*.label
>
> match
>
> mri/wmparc.mgz
>
> mismatch
>
> surf/qsphere.nofix
>
> surf/rh.sphere
>
> mismatch
>
> mri/orig/001.mgz
>
> mismatch
>
> mri/transforms/talairach.m3z
>
> match
>
> mri/transforms/talairach.m3z.inv.x.mgz
>
> mri/transforms/talairach.m3z.inv.y.mgz
>
> mri/transforms/talairach.m3z.inv.z.mgz
>
> mismatch
>
> mismatch
>
> mismatch
>
>
>
> Best - Don
>
>
>
>
>
> Don Krieger, Ph.D.
>
> Department of Neurological Surgery
>
> University of Pittsburgh
>
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Re: [Freesurfer] spot checking results

[dgw]

Don,

Running FreeSurfer on two different versions of any operating system 
will not produce the same results. If you want the same results, you 
must use exactly the same version of an operating system for all of an 
analysis.

hth
d

On 2/5/16 8:29 PM, Krieger, Donald N. wrote:
> Dear List,
>
> I have run recon-all –all on the same scan on two different machines
> likely running two different versions of Linux but in any case the runs
> were done with different numbers of cores.
>
> I  haven’t done anything fancy to compare that the results are identical
> except for some spot checks of individual files with md5sum.
>
> label/lh.BA4a.label shows up the same on both.
>
> mri/wmparc.mgz does not.
>
> Your comments would be welcome.
>
> Is there something about the non-ascii files, e.g. wmparc.mgz, which
> would make them show different checksums, e.g. inclusion of a processing
> time or some such?
>
> Do you have experience or suggestions for convincing ourselves that we
> are getting the same answers on different machines?
>
> ???
>
> Thanks - Don
>
>
>
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Re: [Freesurfer] Zero angle for retinotopy

[dgw]

Hi,

I know Doug is away, so he may correct me later, but I believe it
doesn't matter, as long as it is consistent across runs, and you know
what it is. It will just determine where the angle 0 activity goes (in
a color map etc.). The way FS-FAST does the mapping it just may mean
your colors don't line up with others.

hth
d

On Thu, Feb 4, 2016 at 11:52 PM,   wrote:
> Dear all,
>
>
>
> I am wondering about what the zero angle for retinotopy corresponds to in
> retinotopy analysis. I mean corresponding to the wedge being at zero angle
> in circular coordinate map (horizontal) or vertical up?
>
>
>
> Thank you,
>
> Best,
>
>
>
>
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Re: [Freesurfer] Viewing nifti file in freeview

[dgw]

Amanda,

Is there a progress bar still running? Have you tried changing the window min 
max fields?

hth
d

Sent from my Phone

> On Feb 4, 2016, at 06:46, Worker, Amanda  wrote:
> 
> Hi All,
> 
> 
> I was hoping someone could help with an issue that I'm having that I'm sure 
> has a simple explanation. I have a proton density map in nifti format that I 
> am trying to convert to mgz using mri_convert. 
> 
> 
> However,  when I load the original nifti file into freeview, I get a blank 
> screen and the same when I try to load the converted .mgz - but I have no 
> issue with loading this file into fslview. Other nifti and .mgz files are 
> also loading fine into freeview.
> 
> 
> Has anyone seen this problem before?
> 
> 
> Thanks,
> 
> 
> Amanda
> 
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Re: [Freesurfer] Segmentation depends on image file format

[dgw]

What software did you use to generate the NIFTI files? Many of the
converters do different things to the axes of the data, and this does
affect results.

hth
d

On Thu, Jan 28, 2016 at 8:49 AM, Parzer, Peter
 wrote:
> Hi,
>
> we have brain images stored as DICOM and as NIFTI files. For some time we 
> used to import the NIFTI files to freesurfer for segmentation. I was curious 
> if it makes a difference if we would import the DICOM files directly, and was 
> surprised that it actually did. Here are the commands we used:
>
> # Import DICOM files
> recon-all -s 3003PC_dcm -i 
> ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm
>
> # Convert DICOM to NIFTI and import NIFTI file
> mri_convert ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm 
> 3003PC.nii.gz
> recon-all -s 3003PC_nii -i 3003PC.nii.gz
>
> # Segmentation of DICOM file import
> recon-all -s 3003PC_dcm -all
>
> # Segmentation of NIFTI file import
> recon-all -s 3003PC_nii -all
>
> Here are the first 3 volumes from aseg.stats for 3003PC_dcm (DICOM import)
>
>   1   4  5612 5611.8  Left-Lateral-Ventricle27.6355
> 12.8465 8.93.85.
>   2   5   452  452.2  Left-Inf-Lat-Vent 42.1100
> 14.9377 7.86.79.
>   3   7 1376513765.1  Left-Cerebellum-White-Matter  87.7808 
> 6.600836.   109.73.
>
> and here the the first 3 volumes for 3003PC_nii (NIFTI import)
>
>   1   4  5582 5582.2  Left-Lateral-Ventricle27.4507
> 12.7212 8.93.85.
>   2   5   421  421.1  Left-Inf-Lat-Vent 40.8032
> 14.6554 7.83.76.
>   3   7 1389913898.6  Left-Cerebellum-White-Matter  87.6707 
> 6.753936.   109.73.
>
> The differences are small but I think there should be no differences at all. 
> Has someone an explanation for this differences and which file format is 
> better?
>
> Greetings
> Peter
>
> P. S.: Our system: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on 
> Ubuntu 14.04
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[Freesurfer] separate non-contiguous labels

[dgw]

Hi,

I want to separate each label in the Yeo parcellations into each of
their separate contiguous labels. Is there a command, which can do
this in Freesurfer?

Example lh.yeo7.annot
the network 7 label has 5 non-contiguous components

Is there a command to separate these into 5 separate labels?

Thank You,
Dan
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Re: [Freesurfer] (no subject)

[dgw]

Jasmin,

Did you follow the instructions from the wiki:

https://surfer.nmr.mgh.harvard.edu/fswiki/QuickInstall
which links to this mac specific page.
https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall

?

hth
d

On Thu, Jan 14, 2016 at 5:10 PM, Jasmin Alves  wrote:
> Jasmins-MacBook-Pro:freesurfer jasminalves$ ls -l
> $FREESURFER_HOME/bin/tksurfer
>
> -rwxr-xr-x  1 root  wheel  103 May 14  2013
> /Applications/freesurfer/bin/tksurfer
>
>
> Jasmins-MacBook-Pro:freesurfer jasminalves$ $> freeview -v
> $SUBJECTS_DIR/bert/mri/brainmask.mgz -v
> $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f
> $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f
> $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f
> $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f
> $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red
>
> -bash: freeview: Permission denied
>
>
> On Thu, Jan 14, 2016 at 2:04 PM, Douglas N Greve 
> wrote:
>>
>> Jasmin, can you just cut and paste it into the email?
>>
>> On 01/14/2016 04:59 PM, Jasmin Alves wrote:
>> > Here is the output to the ls command
>> >
>> > On Thu, Jan 14, 2016 at 1:55 PM, Jasmin Alves > > > wrote:
>> >
>> > Hi Dr. Greve,
>> >
>> > I am still receiving the same message that I am denied access to
>> > freeview. Is there anything I can do?
>> >
>> > Thanks,
>> > Jasmin
>> >
>> > On Thu, Jan 14, 2016 at 1:22 PM, Douglas N Greve
>> > mailto:gr...@nmr.mgh.harvard.edu>>
>> > wrote:
>> >
>> > Hi Jasmin, do you have permission to execute FS commands? What
>> > is the
>> > result of
>> > ls -l $FREESURFER_HOME/bin/tksurfer
>> >
>> >
>> >
>> > On 01/14/2016 04:16 PM, Jasmin Alves wrote:
>> > > Hello,
>> > >
>> > > I recently downloaded freesurfer on my mac with a Yosemite
>> > operating
>> > > system. The application itself appears to work, however I am
>> > not able
>> > > to use the command line to do any of the testing free surfer
>> > commands,
>> > > as I keep getting a access denied. I have attached a
>> > screenshot. Your
>> > > help would be very useful.
>> > >
>> > > Thank you,
>> > > Jasmin
>> > >
>> > > --
>> > > Jasmin Alves
>> > > Predoctoral Student
>> > > Medical Biology Graduate Program
>> > > University of Southern California
>> > > jal...@usc.edu 
>> > >
>> > >
>> > >
>> > >
>> > > ___
>> > > Freesurfer mailing list
>> > > Freesurfer@nmr.mgh.harvard.edu
>> > 
>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > gr...@nmr.mgh.harvard.edu 
>> > Phone Number: 617-724-2358 
>> > Fax: 617-726-7422 
>> >
>> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> > 
>> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> > 
>> > Outgoing:
>> > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> >
>> > ___
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>> > Freesurfer@nmr.mgh.harvard.edu
>> > 
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> >
>> > The information in this e-mail is intended only for the person
>> > to whom it is
>> > addressed. If you believe this e-mail was sent to you in error
>> > and the e-mail
>> > contains patient information, please contact the Partners
>> > Compliance HelpLine at
>> > http://www.partners.org/complianceline . If the e-mail was
>> > sent to you in error
>> > but does not contain patient information, please contact the
>> > sender and properly
>> > dispose of the e-mail.
>> >
>> >
>> >
>> >
>> > --
>> > Jasmin Alves
>> > Predoctoral Student
>> > Medical Biology Graduate Program
>> > University of Southern California
>> > jal...@usc.edu 
>> >
>> >
>> >
>> >
>> > --
>> > Jasmin Alves
>> > Predoctoral Student
>> > Medical Biology Graduate Program
>> > University of Southern California
>> > jal...@usc.edu 
>> >
>> >
>> >
>> > ___
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>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.n

Re: [Freesurfer] searchable Destrieux atlas by recon all labels?

[dgw]

Hi Andrea,

As far as I know no.

Additionally, i don't think it makes a lot of sense to do, because the 
two parcellations are created in fsaverage space, and while there are 
morphings etc. that are possible these tricks will always introduce 
errors etc. Additionally MNI space is defined in a completely different 
way to Freesurfer space, and so translating the one two the other is 
strange, because in FS you have locations on a surface while in MNI they 
are 3d coordinates. Occasionally frustrating reviewers demand MNI 
coordinates, likely not realizing that in that translation they are 
being provided with strange data, and we have to send them something, 
but overall, I find that picking the atlas/space which makes sense for 
that question is the best place to start.

hth
d

On 1/9/16 12:40 PM, Andrea Bozoki wrote:
> Thank you. This is helpful.
>
> As to the broader question: is there truly no interactive, online atlas
> that uses either the Destrieux or Duvernoy parcellation scheme to examine
> the landmark boundaries with respect to, say, MNI space?
>
> Thanks,
> Andrea
>
> On 1/7/16, 4:26 PM, "dgw"  wrote:
>
>> freeview partial solution
>>
>> If this is important to you, you could write a quick script to do this
>> for you:
>>
>> 1. mri_annotation2label to output all labels
>>
>> 2. write a script to launch freeview and load all of the labels
>> (reading the color and applying it from the FS ctab file)
>>
>> e.g. freeview -f
>> surf/lh.inflated:label=label/lh.BA1.label:label_color=255,0,0 &
>>
>> 3 you could then scroll through and click all of them off, and then
>> click to load each one individually.
>>
>> or perhaps a new option could be added to the surface label called
>> :label_opacity=0 (which would uncheck the view label option).
>>
>> hth
>> d
>>
>> On Thu, Jan 7, 2016 at 3:53 PM, Bruce Fischl 
>> wrote:
>>> Hi Andrea
>>>
>>> I'm not sure what you mean but I'm pretty certain the answer is "no".
>>>
>>> sorry
>>> Bruce
>>>
>>> On Thu, 7 Jan 2016, Andrea Bozoki wrote:
>>>
>>>> Is there any interactive or searchable version of the Destrieux atlas
>>>> parcellations (the ones used by aparc.a2009s.annot)?
>>>>
>>>> It would be very helpful to be able to toggle back and forth between
>>>> individual recon-all labels and a color atlas of the relevant region
>>>> when
>>>> examining ROI-based quantitative output (output that is not visual).
>>>>
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Andrea B.
>>>>
>>>>
>>>>
>>>>
>>>
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
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>>> in
>>> error
>>> but does not contain patient information, please contact the sender and
>>> properly
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>>
>
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Re: [Freesurfer] searchable Destrieux atlas by recon all labels?

[dgw]

freeview partial solution

If this is important to you, you could write a quick script to do this for you:

1. mri_annotation2label to output all labels

2. write a script to launch freeview and load all of the labels
(reading the color and applying it from the FS ctab file)

e.g. freeview -f surf/lh.inflated:label=label/lh.BA1.label:label_color=255,0,0 &

3 you could then scroll through and click all of them off, and then
click to load each one individually.

or perhaps a new option could be added to the surface label called
:label_opacity=0 (which would uncheck the view label option).

hth
d

On Thu, Jan 7, 2016 at 3:53 PM, Bruce Fischl  wrote:
> Hi Andrea
>
> I'm not sure what you mean but I'm pretty certain the answer is "no".
>
> sorry
> Bruce
>
> On Thu, 7 Jan 2016, Andrea Bozoki wrote:
>
>> Is there any interactive or searchable version of the Destrieux atlas
>> parcellations (the ones used by aparc.a2009s.annot)?
>>
>> It would be very helpful to be able to toggle back and forth between
>> individual recon-all labels and a color atlas of the relevant region when
>> examining ROI-based quantitative output (output that is not visual).
>>
>>
>>
>> Thanks,
>>
>> Andrea B.
>>
>>
>>
>>
>
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Re: [Freesurfer] Drawing a circle around a vertex on a surface

[dgw]

The only code I am aware of for doing this is in mne-python.

hth
d

On 11/8/15 5:36 PM, Reza Rajimehr wrote:
> Hi,
>
> I want to draw a circle around a vertex on the smoothwm or pial surface,
> with a particular radius (e.g. 10 mm), fill the circular region and save it
> as a label file, then repeat this for all the vertices on the surface. I
> need this for doing a searchlight analysis. Does anyone have a script/code
> for it?
>
> I know that mris_pmake (using Dijkstra's algorithm) can be used for this
> purpose, but I don't know exactly how to make it to work in a script for
> drawing circular ROIs.
>
> Thanks for any help!
>
> Reza
>
>
>
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Re: [Freesurfer] Mac Version and Output differs

[dgw]

Dear Kasper,

This is due to the different operating systems you are running not
differences in the computers. Your iMac is running ~10.7 and your
MacPro is running ~10.9.
You should always run your analysis on the same operating system,
however you should get no differences on different computers with the
same operating system.

hth
d

On Mon, Nov 2, 2015 at 11:47 AM, Kasper Jessen  wrote:
> Dear FreeSurfer group,
>
> I have tested the data output on the same subjects using the same FreeSurfer
> version but on different machines, a MacPro and a iMac. The output are
> different, which argues that it is important to run freesurfer on the same
> computer on all your subjects.
>
> Is it due to a randomisation in freesurfer (maybe because of seed points)?
> Is it possible to get the same results even though you run in on different
> computers?
>
> MacPro:
> build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0
> Darwin mac-pro-2014.regionh.top.local 13.4.0 Darwin Kernel Version 13.4.0:
> Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64
>
> iMac:
> build-stamp.txt: freesurfer-Darwin-lion-stable-pub-v5.3.0
> Darwin Nikolajs-iMac.local 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23
> 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64
>
> Best regards,
> Kasper Jessen
>
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Re: [Freesurfer] How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?

[dgw]

Hi Emad,

The only problems, which I have run into is major weaknesses in dcm2nii:
1. You must have write permissions on the directory the files are 
located in.
2. dcm2nii cannot work on symbolically linked files.

Therefore, first copy the files to your own analysis workspace: e.g. 
/cluster//
then run dcm2nii.
With that I have no problems.

hth
d

On 10/30/15 10:28 AM, Emad Ahmadi wrote:
> Hi Freesurfer experts,
>
> I hope you’re all enjoying your day!
>
> Working in Launchpad, I want to extract the bvals/bvecs from DTI dicoms
> obtained at Martinos Center. The dicoms have the following format:
>
> MR1.3.12.2.1107.5.2.32.35006.2010052613553219211129919
> MR1.3.12.2.1107.5.2.32.35006.2010052613553736471330196
> MR1.3.12.2.1107.5.2.32.35006.201005261355429098330464
> ...
>
> I receive error when I run dcm2niix (to extract the b values and b
> vectors):
>
> Command:
> dcm2niix -f dti 
>
> The error I receive:
>
> Warning: output folder invalid
> MR1.3.12.2.1107.5.2.32.35006.2010052614044051320551992 will try
> Error: unable to find any DICOM images in
> Conversion required 0.00 seconds.
>
> When I do the following steps to generate “treatable” dicoms, dcm2niix
> recognizes these dicoms:
>
> 1. copy Martinos Center dicoms to my local Mac
> 2. import dicoms into OsiriX
> 3. Export them as dicoms
> 4. copy the OsiriX-exported dicoms back to Launchpad
> 5. Run dcm2niix on the new dicoms
>
> Since this copying back and forth takes a lot of time, I need a better
> way to convert the “crazy” Martinos Center dicoms into the “treatable” ones!
>
> I would really appreciate your help.
>
> Best,
> Emad
>
>
> Emad Ahmadi, MD
> ---
> Research Fellow
> Department of Radiology
> Massachusetts General Hospital
> Harvard Medical School
>
> 25 New Chardon Street, Suite 400
> Boston, MA 02114
> Tel: 617 726 5237
> Email: e...@nmr.mgh.harvard.edu 
>
>
>
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Re: [Freesurfer] Head circumference

[dgw]

Hi John,

There is nothing, which I can think of. What do you want the head
circumference for (perhaps we can get you a different measure, which
will help)?

hth
d

On Sat, Oct 24, 2015 at 2:22 PM, John Anderson  wrote:
> Dear FS experts,
> I want to inquire if there is any tool or method in Freesurfer that can help
> to calculate the head circumference from MPRAGE ?
> Thanks for any advice!
>
>
>
> Bests,
> John
>
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[Freesurfer] FSFAST -per-run question

[dgw]

Hi,

I know that -per-run is the recommended motion correction option, and
that it uses the middle frame as the reference for motion correction
for each run. I was wondering, if there is a reference, or explanation
as to why that was chosen and not some other timepoint.

Thanks,
d
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Re: [Freesurfer] Viewing vitamin E capsules?

[dgw]

Why not just open the T1.mgz and load the FreeSurfer surfaces? Is there 
a more specific goal?

hth
d

On 10/19/15 10:56 AM, Hutton, Seth wrote:
> Dear users,
>
> I have been using FreeSurfer for a while now, but am working in a new
> lab and their goals fall outside of my realm of experience.
> We are using both MRI imaging as well as FNIRs. We have multiple vitamin
> E capsules placed during both and would like to be able to view them in
> FreeSurfer so that we can better estimate the projected cortical
> localization of these capsules.
> Using the generic recon-all -s -i -all we are unable to see our
> capsules, as they are most likely eliminated during the skull strip
> step. I see that I can change the threshold with "-wsmore", but am
> wondering if this is really the best way to accomplish what we are
> trying to do.
> Is there any way to include our capsules without excluding the skull
> strip? If not could how would you recommend adjusting the threshold.
> I tried excluding the skulls trip step with
> recon-all -s -i -autorecon1 -noskullstrip
> but then when I tried to view it using free view it was unable to open
> due to the lack of the brain mask.mgz.
>
> Thank you so much for your time and consideration,
> Seth H
>
> **
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues
>
>
>
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Re: [Freesurfer] Error Messages for Accessing Bin

[dgw]

what operating system are you running? 64 bit or 32 bit?
Why did you decide to install version 5.0 instead of the current stable 5.3?

hth
d

On Mon, Oct 5, 2015 at 5:41 PM, Timothy Le  wrote:
> Hi,
> From the following output, how should I proceed?
> Thank you very much
> Timothy Le
>
> On Oct 2, 2015, at 11:55 AM, Timothy Quang-Tin Le  wrote:
>
> Hi,
> Thank you very much for your response. The output of that command was:
>
> tle7@sni-vcs-gotlib:~$ ls -l /home/tle7/freesurfer/bin/mri_convert
> -rwxrwx--x 1 tle7 stanford 1672136 Aug 15  2010
> /home/tle7/freesurfer/bin/mri_convert
> tle7@sni-vcs-gotlib:~$
>
>
> On Fri, Oct 2, 2015 at 10:39 AM, dgw  wrote:
>>
>> Timothy,
>>
>> What is the output of this command:
>>
>> ls -l /home/tle7/freesurfer/bin/mri_convert
>>
>> ?
>>
>> hth
>> d
>>
>> On Fri, Oct 2, 2015 at 1:36 PM, Timothy Quang-Tin Le 
>> wrote:
>> > Hi,
>> > I tried the chmod command, but it did not work. How I check that I've
>> > downloaded the correct version?
>> > Thank you very much
>> > Timothy
>> >
>> > On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl
>> > 
>> > wrote:
>> >>
>> >> can you try chmod a+x on one of them and see if it can then be
>> >> executed?
>> >> e.g.:
>> >>
>> >> chmod a+x  /home/tle7/freesurfer/bin/mri_convert
>> >>  /home/tle7/freesurfer/bin/mri_convert
>> >>
>> >> and see if you get an error. If not, you probably downloaded the wrong
>> >> hardware version
>> >> cheers
>> >> Bruce
>> >>
>> >>
>> >>
>> >> On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote:
>> >>
>> >>>
>> >>>   Hello,
>> >>> When I run the command "sFSstart" on version 5.0.0, I am receiving the
>> >>> messages below. Would you please explain to me what the problem is? It
>> >>> seems like there is trouble accessing the bin.
>> >>> Thank you
>> >>>
>> >>>  freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 
>> >>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>> >>> FREESURFER_HOME   /home/tle7/freesurfer
>> >>> FSFAST_HOME   /home/tle7/freesurfer/fsfast
>> >>> FSF_OUTPUT_FORMAT nii
>> >>> SUBJECTS_DIR  /home/tle7/freesurfer/subjects
>> >>> MNI_DIR   /home/tle7/freesurfer/mni
>> >>> tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2
>> >>> studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter
>> >>> H 0
>> >>> checking sid number 00152-DT2
>> >>> 1
>> >>>
>> >>> 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
>> >>> Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>> >>> Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>> >>> INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects
>> >>> Actual FREESURFER_HOME /home/tle7/freesurfer
>> >>> Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP
>> >>> Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>> >>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>> >>> not executable.
>> >>> /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file
>> >>> not executable.
>> >>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>> >>> not executable.
>> >>> /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not
>> >>> executable.
>> >>> /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file
>> >>> not executable.
>> >>> /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary
>> >>> file not executable.
>> >>> /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary
>> >>> file not executable.
>>

Re: [Freesurfer] Error using selexavg3-sess

[dgw]

Hi Keji,

Without more details, it may be hard to guess. I suspect it might be 
that not all of the conditions in your analysis happened during the 
experiment for those participants (e.g. some sort of button press).

hth
d

On 10/2/15 5:47 PM, Morenikeji Adebayo wrote:
> Just following up on this - thanks!
>
>> On Sep 29, 2015, at 1:29 PM, Morenikeji Adebayo
>> mailto:k...@nmr.mgh.harvard.edu>> wrote:
>>
>> Hi there,
>>
>> I’m running into difficulty executing the “selexavg3-sess” command for
>> a few participants. For example, when I run the command:
>>
>> *foreach c(lh rh mni305)*
>> *selxavg3-sess -analysis analysis_encoding_stimXmem.$c-s
>> nmasa_045_130621 -d . -no-preproc*
>> *end*
>>
>>
>> I get the following error:
>>
>>
>> *Error using svd*
>> *Input to SVD must not contain NaN or Inf.*
>> *
>> *
>> *Error in cond (line 36)*
>> *s = svd(A);*
>> *
>> *
>> *Error in fast_selxavg3 (line 279)*
>> *  XCond = cond(XtX);*
>>
>> Any help on this error would be much appreciated!
>>
>> Thanks,
>> Keji
>>
>> ---
>> Morenikeji Adebayo
>> Clinical Research Coordinator
>> Department of Psychiatric Neuroscience
>> Massachusetts General Hospital
>> (p) 617.643.6347
>> k...@nmr.mgh.harvard.edu 
>>
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>
> ---
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> Clinical Research Coordinator
> Department of Psychiatric Neuroscience
> Massachusetts General Hospital
> (p) 617.643.6347
> k...@nmr.mgh.harvard.edu 
>
>
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Re: [Freesurfer] Error Messages for Accessing Bin

[dgw]

Timothy,

What is the output of this command:

ls -l /home/tle7/freesurfer/bin/mri_convert

?

hth
d

On Fri, Oct 2, 2015 at 1:36 PM, Timothy Quang-Tin Le  wrote:
> Hi,
> I tried the chmod command, but it did not work. How I check that I've
> downloaded the correct version?
> Thank you very much
> Timothy
>
> On Thu, Oct 1, 2015 at 8:10 AM, Bruce Fischl 
> wrote:
>>
>> can you try chmod a+x on one of them and see if it can then be executed?
>> e.g.:
>>
>> chmod a+x  /home/tle7/freesurfer/bin/mri_convert
>>  /home/tle7/freesurfer/bin/mri_convert
>>
>> and see if you get an error. If not, you probably downloaded the wrong
>> hardware version
>> cheers
>> Bruce
>>
>>
>>
>> On Tue, 29 Sep 2015, Timothy Quang-Tin Le wrote:
>>
>>>
>>>   Hello,
>>> When I run the command "sFSstart" on version 5.0.0, I am receiving the
>>> messages below. Would you please explain to me what the problem is? It
>>> seems like there is trouble accessing the bin.
>>> Thank you
>>>
>>>  freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 
>>> Setting up environment for FreeSurfer/FS-FAST (and FSL)
>>> FREESURFER_HOME   /home/tle7/freesurfer
>>> FSFAST_HOME   /home/tle7/freesurfer/fsfast
>>> FSF_OUTPUT_FORMAT nii
>>> SUBJECTS_DIR  /home/tle7/freesurfer/subjects
>>> MNI_DIR   /home/tle7/freesurfer/mni
>>> tle7@sni-vcs-gotlib:~$ sFSstart practicemotherdaughter 00152-DT2
>>> studyPath /home/tle7/freesurfer/subjects/practicemotherdaughter
>>> H 0
>>> checking sid number 00152-DT2
>>> 1
>>> 00152-DT2/MR.1.2.840.113619.2.283.4120.7575399.15360.1319907833.100.dcm
>>> Subject Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>>> Current Stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0
>>> INFO: SUBJECTS_DIR is /home/tle7/freesurfer/subjects
>>> Actual FREESURFER_HOME /home/tle7/freesurfer
>>> Linux sni-vcs-gotlib.stanford.edu 3.13.0-61-generic #100-Ubuntu SMP
>>> Wed Jul 29 11:21:34 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux
>>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/flirt.fsl: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mri_convert: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/tkregister2_cmdl: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_normalize: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_watershed: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_gcut: Exec format error. Binary file not
>>> executable.
>>> /home/tle7/freesurfer/bin/mri_segment: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mri_label2label: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_em_register: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_ca_normalize: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_ca_register: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_ca_label: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mri_pretess: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mri_fill: Exec format error. Binary file not
>>> executable.
>>> /home/tle7/freesurfer/bin/mri_tessellate: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mri_concatenate_lta: Exec format error.
>>> Binary file not executable.
>>> /home/tle7/freesurfer/bin/mri_normalize_tp2: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_smooth: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mris_inflate: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mris_curvature: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_sphere: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mris_fix_topology: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_topo_fixer: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_ca_label: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_euler_number: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_make_surfaces: Exec format error.
>>> Binary file not executable.
>>> /home/tle7/freesurfer/bin/mris_register: Exec format error. Binary
>>> file not executable.
>>> /home/tle7/freesurfer/bin/mris_volmask: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mris_anatomical_stats: Exec format error.
>>> Binary file not executable.
>>> /home/tle7/freesurfer/bin/mrisp_paint: Exec format error. Binary file
>>> not executable.
>>> /home/tle7/freesurfer/bin/mris_curvat

Re: [Freesurfer] White Matter Edits vs. Control Points, & third party software

[dgw]

Alberto,

I included detailed replies below, but I have a question before you get 
to those. Why don't you want to follow the FreeSurfer techniques for 
reconstruction? You suggested several other ways, but I don't understand 
your motivation for not wanting to follow the instructions for FreeSurfer.

On 10/2/15 5:49 AM, Julio Alberto González Torre wrote:
> I have some questions about how to manually correct the white matter
> regions.
>
> It's the same manually edit the volume "brainmask.mgz" and use control
> points?Would I get the same result? My intention is not to use control
> points, but directly replace the voxels that have not been classified as
> white matter with the value 110. Is it right to do this?

Why don't you want to use control points? They do more than replace the 
value with 110. They let FreeSurfer know that that voxel is definitely 
white matter even though the intensity is different. It can then tweak 
what it sees as white matter locally in that space and get you a good 
measure of the border. Remember the border is likely to occur in the 
middle of voxels with partial voluming effects, where the intensity is 
not 110, and also where you should not make the volume 110.

>
> My second question is: Is it possible to edit the volumes with a third
> party program? My intention here is to turn the volume "brainmask.mgz"
> to "brainmask.nii" using "mri_convert" command. Then edit the values of
> the voxels manually with a third party software or painting tool, and
> finally, turn the volume back to "brainmask.mgz", replace the file in
> their respective directory, and finally execute "-autorecon2- wm". Is it
> right to do this? Or this may compromise my data?

While I am not a FreeSurfer dev, I would strongly discourage you from 
doing this. First, it will be easier to get help, troubleshoot and do 
things properly, if follow the FreeSurfer techniques, plus you will need 
their tools to do any corrections to the Talairach etc. Second, the 
NIFTI format is pretty bad and lacks a lot of data which the mgz format 
preserves.

>
> Thanks in advance,
> Alberto.
>
>
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Re: [Freesurfer] freeview crash with emutls_get_address but work from command line on MacOS X 10.10.5

[dgw]

But don't you just save the FDR correction to a file then load that in freeview?
I imagine the problem has to do with MATLAB changing the way it works on OSX.
It doesn't use X11 anymore, unlike on linux (this is supposition). I
would say the
best bet would be to do the FDR correction in MATLAB, then save it to
a file that
you can load in Freeview.

hth
d

On Tue, Sep 15, 2015 at 12:58 PM, Knut Jørgen Bjuland
 wrote:
> It works from the terminal windows. I start from within Matlab, to get FDR
> correction as Freeview do not have it. And I use an FDR correction that uses
> data from both hemisphere. I have managed to get it working under Ubuntu
> 14.04.3.
>
>
>
> On 15 Sep 2015, at 18:49, dgw  wrote:
>
> Starting Freeview from MATLAB is an odd thing to do. What happens if
> you just start freeview normally?
>
> hth
> D
>
> On Tue, Sep 15, 2015 at 12:21 PM, Knut Jørgen Bjuland
>  wrote:
>
> When I load Freeview developmental version from Freesurver developmental
> version from Matlab 2015b.
> I used this command to load freeview.
>
> fdrthresh=sprintf('%s,%s',num2str(lowerfdr),num2str(upperfdr));
>
>commandline=sprintf('freeview -f
> %s/%s/surf/%s.%s:annot=aparc.annot:annot_outline=1:overlay=%s:overlay_threshold=%s
> &',SUBJECTS_DIR,template,hemi,surface,overlayfile,fdrthresh);
>
> system(commandline)
>
>
>
>
> I get this error.dyld: lazy symbol binding failed: Symbol not found:
> ___emutls_get_address
>  Referenced from:
> /Applications/freesurfer//Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
>  Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>  Referenced from:
> /Applications/freesurfer//Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
>  Expected in: /usr/lib/libSystem.B.dylib
>
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Caught signal number 5 TRAP
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
> find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Unknown Name on a darwin12. named Knuts-MacBook-Pro.local by
> knutjorgenbjulan Tue Sep 15 18:16:13 2015
> [0]PETSC ERROR: Libraries linked from
> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
> [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown
> file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
> find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> --

Re: [Freesurfer] freeview crash with emutls_get_address but work from command line on MacOS X 10.10.5

[dgw]

Starting Freeview from MATLAB is an odd thing to do. What happens if
you just start freeview normally?

hth
D

On Tue, Sep 15, 2015 at 12:21 PM, Knut Jørgen Bjuland
 wrote:
> When I load Freeview developmental version from Freesurver developmental
> version from Matlab 2015b.
> I used this command to load freeview.
>
> fdrthresh=sprintf('%s,%s',num2str(lowerfdr),num2str(upperfdr));
>
> commandline=sprintf('freeview -f
> %s/%s/surf/%s.%s:annot=aparc.annot:annot_outline=1:overlay=%s:overlay_threshold=%s
> &',SUBJECTS_DIR,template,hemi,surface,overlayfile,fdrthresh);
>
> system(commandline)
>
>
>
>
> I get this error.dyld: lazy symbol binding failed: Symbol not found:
> ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer//Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from:
> /Applications/freesurfer//Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Caught signal number 5 TRAP
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
> find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Unknown Name on a darwin12. named Knuts-MacBook-Pro.local by
> knutjorgenbjulan Tue Sep 15 18:16:13 2015
> [0]PETSC ERROR: Libraries linked from
> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
> [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown
> file
> [unset]: aborting job:
> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> probably memory access out of range
> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
> [0]PETSC ERROR: or see
> http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC
> ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to
> find memory corruption errors
> [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and
> run
> [0]PETSC ERROR: to get more information on the crash.
> [0]PETSC ERROR: - Error Message
> 
> [0]PETSC ERROR: Signal received!
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26
> CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124
> [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> [0]PETSC ERROR: See docs/index.html for manual pages.
> [0]PETSC ERROR:
> 
> [0]PETSC ERROR: Unknown Name on a darwin12. named Knuts-MacBook-Pro.local by
> knutjorgenbjulan Tue Sep 15 18:16:13 2015
> [0]PETSC ERROR: Libraries linked from
> /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt
> [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012
> [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc
> --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1
> --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3
> CXXOPTFLAGS=-O3 FOPTFLAGS=-O3
> [0]PETSC ERROR:
> --

Re: [Freesurfer] Questions about the correction methods in Surfstat

[dgw]

Hi Feng,

This is not the surfstat list. You may want to check their webpage to
see how to get help and documentation.

hth
d

On Sun, Sep 13, 2015 at 9:36 AM, chenhf_uestc  wrote:
> Dear Surfstat Users,
>
> I have a question about the RFT correction method in the
> Surfstat(http://www.math.mcgill.ca/keith/surfstat/).
> In the online manual, the command to perform RFT correction is as follows:
> [ pval, peak, clus ] = SurfStatP( slm, mask );
>
> pval.P contains P-values for peaks, and pval.C contains P-values for
> clusters. This special structure is recognised by SurfStatView which draws
> the figure in a special way:
>
> SurfStatView( pval, avsurf, 'Males-females removing age' );
>
> The output figure is attached. In the colorbar of the figure, left
> represents cluster corrected p value and right one represents the vertex
> corrected p value, right? So, the warm color region in the figure can be
> survived by the RFT vertex correction, and the cool color region in the
> figure can be survived by the RFT cluster correction, right? If so, the
> regions with either warm or cool color region that can be survived after
> correction. When I report the results, I can report the regions with warm
> color (vertex level correction) or report the regions with cool color
> (cluster level correction), right?
>
> In addtion, how can I understand the region overlapped by the warm and cool
> color (like he postier cingulate cortex), can simultaneously pass double
> correction of vertex level and cluster level?
>
> The final question is about the RFT cluster correction method, in the SPM or
> other software (like REST). Generally, on the cluster level correction, you
> should be based on a voxel (vertex) uncorrected height threshold of e.g.
> p<0.001 combined with a RFT-correlated cluster threshould of e.g., p<0.05,
> right? What is the detailed correction procedure in the Surfstat software?
>
> Any help would be greatly appreciate.
>
> Best,
> Feng
>
>
>
>
>
>
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Re: [Freesurfer] Did not find any volume geometry information in the surface

[dgw]

Eric,

It will be easier to help, if you provide a much more detailed
description of what you did: the full command line, the version of
freesurfer, and all terminal output
(http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting this may help).

hth
D

On Mon, Aug 31, 2015 at 3:27 PM, Erik Lindberg
 wrote:
> Hi,
> I am running mri_glmfit followed by mri_glmfit-sim
>
> running the left hemisphere everything works perfect all the way to the
> visualization in freeview  - then I just chift the command to rh instead -
> running exactly the same command and when I am opening my results in
> freeview everything gets yellow and I get the following error message: Did
> not find any volume geometry information in the surface.
>
> could you please inform me how this can happen?
>
> THANKS
> ERIC
>
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Re: [Freesurfer] Large SA when using pial surface...?

[dgw]

Niels,

Why do you expect the surface area to be the same between the two different
surfaces pial, and white?


hth
d

On Fri, Aug 28, 2015 at 8:23 AM, Gerrits, Niels  wrote:

> Dear Experts,
>
> With your help, I recalculated the surface area, now using the pial
> surface instead of the wm/gm boundary. I am, however, somewhat surprised by
> the discrepancy between my previous and current results, because the
> cortical surface area that is calculated using the pial is surface is
> consistently (a lot) larger than the SA that was calculated using the WM/GM
> boundary (please see below for an example; upper table are the old results;
> lower table are the new results). While computing the new SA measure, FS
> also automatically calculated both volume and thickness. Since these two
> measures are exactly the same as previously when SA was calculated using
> the wm/gm boundary (as was to be expected), I assume that the calculation
> of SA using the pial surface was correctly executed.
>
> Nonetheless, I am wondering: 1) is such a large difference to be expected,
> and 2) what could be a physiological explanation for this discrepancy?
>
> All suggestions are much appreciated!
>
> Best wishes,
> Niels Gerrits
>
> *LH_cuneus_area* *LH_entorhinal_area* *LH_fusiform_area*
> *LH_inferiorparietal_area* *PP_01* 1305 349 2563 3699 *PP_02* 1351 368
> 2989 4803 *PP_03* 1324 490 3489 3963 *PP_04* 1714 518 4107 4473 *PP_05*
> 1573 566 3750 5697 *PP_06* 1419 387 3206 4543 *PP_07* 1249 364 2636 4518
> *PP_08* 1386 362 3174 5105 *PP_09* 1322 562 3239 6264 *PP_10* 1696 517
> 3926 5989 *LH_cuneus_area* *LH_entorhinal_area* *LH_fusiform_area*
> *LH_inferiorparietal_area* *PP_01* 1617 575 3231 4446 *PP_02* 1555 661
> 3970 5983 *PP_03* 1769 886 5059 5143 *PP_04* 1964 809 5402 5662 *PP_05*
> 1788 946 4832 6907 *PP_06* 1752 667 3944 5449 *PP_07* 1595 674 3631 5783
> *PP_08* 1779 634 4074 6364 *PP_09* 1648 912 4353 7395 *PP_10* 1915 816
> 4758 7358
>
>
>
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Re: [Freesurfer] mri_deface

[dgw]

Hi Jürgen,

Personally, I don't think defacing is necessary for most DTI data. 
Assuming your slices don't cover the face (which most DTI data doesn't 
include), I think you are safe to say the data is inherently defaced. 
Others may have other ideas.

hth
d

On 8/7/15 6:53 AM, Jürgen Hänggi wrote:
> Dear FS experts
>
> I have to anonymize T1-w. and DTI images. I run mri_deface for T1-w.
> images successfully,
> but I am wondering whether there is any easy way to also deface DTI
> images with mri_deface or
> whether someone has already defaced DTI images with another tool.
>
> Thanks in advance
> Best regards
> Jürgen Hänggi
>
> ---
>
> Jürgen Hänggi, Ph.D.
>
> Division Neuropsychology
>
> Institute of Psychology
>
> University of Zurich
>
> Binzmuehlestrasse 14, PO Box 25
>
> 8050 Zurich, Switzerland
>
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>
> 0041 76 445 86 84 (phone mobile)
>
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>
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>
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>
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>
> http://www.juergenhaenggi.ch (private website)
>
>
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>
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>
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>
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>
>
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[Freesurfer] retinotopy polar

[dgw]

Hi,

I am setting up a polar angle stimulus program, and I am wondering if
there is an option in FS-FAST to analyze data with two opposing wedges
for the polar mapping. Participants can keep fixation better with this
setup, which is why we are aiming to use it.

Thanks,
Dan
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Re: [Freesurfer] hello freesurfer developer~

[dgw]

Hi A-reum,

I think you may be able to get a faster response if you include some 
details about your setup: I would start with the following:

http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
and run bugr.

hth
D

On 7/26/15 5:17 PM, A-reum Min wrote:
> Hi, Bruce
>
> When i use a Qdec, this message(12.png) show up..
> How can i solve this problem?
>
> 2015-07-23 22:57 GMT+09:00 Bruce Fischl  >:
>
> 1. No, each subject has a different #. You can map to fsaverage
> (this is what -qcache does if you specify it for recon-all), then
> they will have the same #.
>
> 2. What result data do you mean?
>
> 3. Yes, although I'll leave the details to Doug (since I don't
> remember how his cluster code works).
>
> 4. The significance doesn't depend on the cluster size unless you do
> multiple comparison corrections (and even then only if you do them a
> certain way)
>
> cheers
> Bruce
>
>
> On Thu, 23 Jul 2015, A-reum Min wrote:
>
> HELLO developer
> I have some question to you..
>
> 1. Every patient is given to the same number of vertex?
>
> 2. When i use a Qdec, How can I get the subject result data?
>
> 3. Could i get the significant vertex’s number, extent of the
> significant area and gray matter volume?
>
> 4. Is it significant blue color which how many connected
> vertex?
>
>
> 2015-05-29 2:03 GMT+09:00 A-reum Min  >:
>hello developer~
> reconstruction is well done, so i'm doing on 'qdec' step..
> Actually, i don't know how to treat the Design menu exactly..
> 
> ---
> Discrete(fixed factors) : diagnosis
> continuous (covariate) : age , Left-Lateral-Ventricle
> 
> ---
> which one click before analyze?
>
> age range is 12years~24years/
> all subjects are adolescent.
> and no outlier in age range.. so.. age (continuous factor) does not
> nasessart?
>
>
> 2015-05-29 1:19 GMT+09:00 A-reum Min  >:
>hello developer~
> reconstruction is well done, so i'm doing on 'qdec' step..
> Actually, i don't know how to treat the Design menu exactly..
> 
> ---
> Discrete(fixed factors) : diagnosis
> continuous (covariate) : age , Left-Lateral-Ventricle
> 
> ---
> which one click before analyze?
>
>
>
> 2015-04-05 21:41 GMT+09:00 Bruce Fischl
> mailto:fis...@nmr.mgh.harvard.edu>>:
>I'm glad it worked out
>Bruce
>On Sun, 5 Apr 2015, A-reum Min wrote:
>
>  Hello Bruce~
>  You're right.. my PISA dicom file header
>  is too short
>  so, freesurfer didn't read it.
>
>  Therefore I use another subjects dicom
>  file and then freesurfer read it!
>
>  thank you for u r adavice to me.
>
>  I really appreciate u
>
>  2015-04-05 7:08 GMT+09:00 Bruce Fischl
>   >:
>Hi  A-reum
>
>the problem is that newer versions
>  of scanner software compress
>dicoms and the version of FS you
>  have doesn't know how to read
>it. So you need to decompress them
>  before passing them to
>recon-all
>
>cheers
>Bruce
>On Sun, 5 Apr 2015, A-reum Min
>  wrote:
>
>  Hello developer~
>
>  Can you summarize what the
>  problem is?
>  ==>
>  my problem is recon-all -i
>  didn't working...
>  so, if i type the recon-all
>  -i~then show up theses
>
>
> 
>  ERROR: 32512, see
>
>  /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out
>  for
>  more details
>  Linux localhost.localdomain
>  2.6.32-504.el6.x86_64 #1
> 

Re: [Freesurfer] unpack error

[dgw]

Was there an error during scanning? The error message looks like there 
was an error during that run and the scan was either aborted by the 
scanner or the scanner crashed on that sequence. Did you check your lab 
notebook?

hth
d

On 7/25/15 2:43 PM, Park, Jung Mi wrote:
> Hi  Freesurfer team
>
> I  did unpacksdcmdir successfully before at Martinos center.
>
> Recently I got error message while I was trying to unpacksdcmdir.
>
> ; Cannot open
> /autofs/cluster/scratch/monday/jungmi/data_parent/0201JB/scan.info
>
> There was some messages in unpack.log;
> INFO: found 4276 Siemens files
> syngo MR B17
> *Could not parse NUMARIS version string syngo MR B17*
> found in dicom tag 18,1020 (len = 3 != 6)
> *WARNING: Run 11 appears to be truncated*
>Files  Found: 224, Files Expected (lRep+1): 1
> FileName
> /cluster/archive/309/siemens/TrioTim-35101-20150325-085700-000970/MR.1.3.12.2.1107.5.2.32.35101.2015032509161179360096424
>
> I found the unpack error from two patients data. I don't understand what
> it happened.
> How can I use these patients data?
>
> Thank you.
>
> Jung Mi
>
>
>
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Re: [Freesurfer] paradigm file

[dgw]

Hi Thuc,

For similar reasons, I program all of my stimulus programs to write a
par file for each run. I recommend you program your stimulus program
to do the same.

HTH
D

On Fri, Jul 24, 2015 at 8:12 AM, Thục Trinh  wrote:
> Hi,
>
> In our experiment, one onset trial will be lasted for 12 seconds, but if
> subject can give the answer sooner within 12 seconds, the next offset trial
> (baseline) will come up. The response time will be recorded.
> So if I have 100 subjects, I have to create 100 paradigm files manually. It
> will cost alot of time. Do you have any suggest to solve this problem.
>
> Thanks
>
> 2015-07-22 20:36 GMT+07:00 Douglas Greve :
>>
>> Each entry in the paradigm file represents a presentation characterized by
>> 4 values:
>> 1. Onset time
>> 2. Stimulus code (integer 0-N)
>> 3. Stimulus duration
>> 4. Weight (usually 1)
>>
>> If each stimulus presentation has a different duration, then that would be
>> indicated in #3
>>
>> doug
>>
>>
>> On 7/22/15 12:23 AM, Thục Trinh wrote:
>>
>> Hello,
>> I'm working on fMRI analysis on flattening brain by using FSFAST tool. In
>> our data, subjects play game: Matrix reasoning. How can I set up the
>> paradigm file if the duration stimulus depends on the Time response of each
>> subject following each trial.
>>
>> Thanks !!
>> Trinh
>>
>>
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Re: [Freesurfer] (no subject)

[dgw]

click on the link at the bottom of every post, or go to the mailing
list link on the wiki:
http://surfer.nmr.mgh.harvard.edu/fswiki
this link on that page:
http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

hth
d

On Thu, Jul 2, 2015 at 8:57 AM, Mojdeh Zamyadi  wrote:
> Could someone please tell me how to unsubscribe from this list? I couldn't
> find it on the website.
> Thanks
>
> On Jul 2, 2015 4:56 AM, "Milde, Christopher"
>  wrote:
>>
>> Dear Freesurfers,
>>
>> I have problems converting .nii.gz files into .mgh files needed e.g. for
>> performing ROI analysis.
>>
>> I used mri_vol2surf and mri_vol2vol to produce .mgh files either to
>> visualize contrast estimates and significance maps on volumes or surfaces
>>
>> I think the problem is due to voxel resolution mismatches between source
>> and registration files but I don't know how to solve this problem.
>>
>> I worked with different registration files: the register.dof6.dat
>> (originally outpu from the preproc-sess) as well as register.dat and
>> register.lta by running bbregister for the template.nii.gz
>>
>>
>>
>> ---
>> here is an example command:
>>
>> # resample to surface
>>
>> mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg
>> $sub/bold/register.lta --projfrac 0.5 \
>>  --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh
>>
>>
>> mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg
>> $sub/bold/register.lta --projfrac 0.5 \
>> >  --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh
>> srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz
>> srcreg = PM_04001/bold/register.lta
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> ProjFrac = 0.5
>> thickness = thickness
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 0
>> INFO: float2int code = 0
>> Done loading volume
>> regio_read_register: loading lta
>> reading extra input line subject PM_04001
>> reading extra input line fscale 0.15
>> WARNING: the voxel resolution in the source volume (1,1,1) differs
>>  from that listed in the registration file (2.29167,2.29167,2.99)
>> Reading surface /home/christopher/subjects/PM_04001/surf/lh.white
>> Done reading source surface
>> Reading thickness /home/christopher/subjects/PM_04001/surf/lh.thickness
>> Done
>> Mapping Source Volume onto Source Subject Surface
>>  1 0.5 0.5 0.5
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 5
>> Writing to PM_04001/bold/lh.sig.mgh
>> Dim: 126553 1 1
>>
>>
>> 
>>
>> Thanks,
>>
>> Christopher
>>
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Re: [Freesurfer] Processing problem in Freesurfer

[dgw]

Hi Guo,

Simply run recon-all again and add the flag -cw256. Then load up the 
orig.mgz and make sure the head is fully visible.

HTH
D
On 7/1/15 9:48 PM, 宾果 wrote:
> Dear Freesurfer team:
> I am here want to ask for your help for some problems in
> Freesurfer when I was processing my data.
>As described below, Freesurfer report :
> ERROR! FOV=320.000 > 256
>Include the flag -cw256 with recon-all!
>Inspect orig.mgz to ensure the head is fully visible.
>   
> so regarding this type of problem, how could I solve it? It seems that
> the FOV of my NIFT image is 320, and it is bigger than 256, which cannot
> be readed and written by orig.mgz. I have tried to open the org.mgz
> file, but it was unaccessible.
>
> so, there are any solutions to deal with this problem? if yes, please
> delivery some instructions to me.
>
> Thank you.
>
>
>
>
>
>
>
>
> --
> Best regards,
>
> Guo Bin/ 宾果
>
>
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Re: [Freesurfer] Read .mgz file matlab

[dgw]

What command did you type?


On Wed, Jun 10, 2015 at 5:32 PM, Mohammed Goryawala  wrote:
> Hello All,
>
> I am trying to read .mgz files into matlab on MacOSX using the MRIread
> command.
>
> It returns me the following error:
>
> SWITCH expression must be a scalar
> or string constant.
>
> Error in load_mgh (line 126)
> switch type
>
> Error in MRIread (line 88)
>   [mri.vol, M, mr_parms, volsz] =
>   load_mgh(fspec,[],[],headeronly);
>
> Error in
> corticalGMConnectivityMatrixFreeSurfer
> (line 6)
> mri = MRIread(MRI_Filename);
>
> Thanks
> Mohammed Goryawala, PhD
> University of Miami
>
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Re: [Freesurfer] Inflated.nofix has holes!!!

[dgw]

Hi Hassan,

You should probably start by working through the tutorials:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tutorials

This one covers that specific topic.
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview

hth
d

On Tue, Jun 9, 2015 at 12:32 PM, Hassan bakhshi
 wrote:
> About visual inspection!!!
> Which images should I check??? And how can I understand the defect in
> images?
>
>
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Re: [Freesurfer] Dev Version

[dgw]

Did you check the permissions? You have to make sure the permissions are 
executable.

HTH
D

On 5/26/15 6:33 AM, Hassan bakhshi wrote:
> Hi
> I downloaded the centos 6 freeview.bin and replaced it into
> $freesurferhome/bin/freeview.bin
>
> but now i cant open freeview, it says that it is not a executable file and
> it is binary.
>
> i wanted to test hippocampal subfields.
>
> Kind regards
>
>
>
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Re: [Freesurfer] Installing FreeSurfer on Fedora 21

[dgw]

Ranjan,

You may want to try installing it on a local hard disk. Do you have
any scratch space you can use on the computer?

HTH,
D

On Tue, Apr 14, 2015 at 5:09 PM, Ranjan Maitra
 wrote:
> Nick,
>
> Thanks! It does match in the gzipped tarball:
>
> ~$ md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
> 6642289df823ebc27de52af57e9b3989  
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz
>
> ~$ md5sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar
> 8cf47fbcd0a675f7832986ee87c2d00f  
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar
>
> I don't think that this matters, but the filesystem is an Inselon OneFS 
> filesystem and is mounted on to my machine via a cifs mount.
>
> Many thanks,
> Ranjan
>
>
>
>
>
>> -Original Message-
>> From: ni...@nmr.mgh.harvard.edu
>> Sent: Tue, 14 Apr 2015 16:26:50 -0400
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Installing FreeSurfer on Fedora 21
>>
>> Ranjan,
>>
>> after downloading, confirm the integrity of the tarball by running
>> md5sum on it.  you should get the following sum:
>>
>> 6642289df823ebc27de52af57e9b3989
>>
>> also, make sure you have at least 4.2GB of space prior to download.
>> some older partitions have a 4GB max size (probably not the case, but
>> thought i'd mention it).
>>
>> Nick
>>
>> On Tue, 2015-04-14 at 12:06 -0800, Ranjan Maitra wrote:
>>> Zeke,
>>>
>>> Thanks!
>>>

 We support centos6 platform but we are currently unaware of any linux
 distributions in which freeview can not open. I dont not have immediate
 access to a Fedora21 system but I will attempt to install one and
 investigate this further. Please allow a day or so for a response.
>>>
>>> Thank you very much!
>>>

 Lastly, it would make me feel a lot better if you could extract the
 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz without
 getting
 any errors. Its possible something is getting corrupted along the way
 which is somehow responsible for this issue.
>>>
>>> I agree with you, but I have tried downloading and unpacking several
>>> times, to no avail. Always the same error/message. (I use wget, but I
>>> don't see why that should be a problem.) I can not see how to get around
>>> this. Do you have any other suggestions as to how to get around this?
>>>
>>> Many thanks,
>>> Ranjan
>>>
>>>
>>>
>>>
 On 04/14/2015 03:15 PM, Ranjan Maitra wrote:
> Zeke,
>
> Thanks again!
>
>> -Original Message-
>> From: zkauf...@nmr.mgh.harvard.edu
>> Sent: Tue, 14 Apr 2015 15:12:06 -0400
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Installing FreeSurfer on Fedora 21
>>
>> Ranjan,
>>
>> Ok, the binaries appear work. So at the present moments the issue
>> appears to only be with libvtkverdict.so.5.6.0
>>
>> 1) What happens if, right before you type the freeview command, you
>> set
>> the LD_LIBRARY_PATH environment variable as follows:
>>
>> (if bash)
>> $> export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6
>> $> freeview
>
> I tried this, to no avail:
>
> ~$ export LD_LIBRARY_PATH=$FREESURFER_HOME/lib/vtk/lib/vtk-5.6
> ~$ freeview
> freeview.bin: error while loading shared libraries:
> libvtkverdict.so.5.6: cannot open shared object file: No such file or
> directory
>
>
>>
>> (if csh)
>> $> setenv LD_LIBRARY_PATH $FREESURFER_HOME/lib/vtk/lib/vtk-5.6
>> $> freeview
>>
>> 2) What is the output when you perform an 'md5sum' on
>> libvtkverdict.so.5.6.0
>>
>> $> cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6
>> $> md5sum libvtkverdict.so.5.6.0
>
> ~$ cd $FREESURFER_HOME/lib/vtk/lib/vtk-5.6
> ~$ md5sum libvtkverdict.so.5.6.0
> 4daa2098074db45b5729d3c68e167f96  libvtkverdict.so.5.6.0
>
> Thanks again!
>
> Best wishes,
> Ranjan
>
>
>>
>>
>> On 04/14/2015 02:55 PM, Ranjan Maitra wrote:
>>> Thanks! It works, in the sense that it goes to completion:
>>>
>>> ~$ mri_convert sample-001.mgz test.mgh
>>> mri_convert sample-001.mgz test.mgh
>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>> reading from sample-001.mgz...
>>> TR=7.25, TE=3.22, TI=600.00, flip angle=7.00
>>> i_ras = (-0, -1, -0)
>>> j_ras = (-0, 0, -1)
>>> k_ras = (-1, 0, 0)
>>> writing to test.mgh...
>>>
>>> ~$
>>>
>>> Best wishes,
>>> Ranjan
>>>
 -Original Message-
 From: zkauf...@nmr.mgh.harvard.edu
 Sent: Tue, 14 Apr 2015 14:44:34 -0400
 To: freesurfer@nmr.mgh.harvard.edu
 Subject: Re: [Freesurfer] Installing FreeSurfer on Fedora 21

 Ranjan,

 What happens when you try to use the mri_convert binary?

 $> cd $FREESURFER_HOME/subjects
 $> mri_convert samp

Re: [Freesurfer] 'current' FSL

[dgw]

If this is the reference, than I think based on the ls -l output, it
is a pretty good guess that it was version 4.1.7

Of course, like Zeke said, this is a complete guess, but based on
plausible information.

HTH
D

On Tue, Mar 31, 2015 at 3:39 PM, Z K  wrote:
> I think he's referring to the convention used in the various
> /usr/pubsw/packages libraries where "current" points to a version
> number. For example as of right now:
>
> /usr/pubsw/packages/fsl/current -> 5.0.7
>
> But there is no real way of knowing the destination of that symlink at
> May 1 2012. At least not that I'm aware of.
>
> -Zeke
>
>
> On 03/31/2015 03:34 PM, dgw wrote:
>> It may help to provide a bit more context e.g. the email/instructions
>> you where you found the reference to 'current' fsl version?
>>
>> HTH,
>> D
>>
>> On Tue, Mar 31, 2015 at 3:31 PM, Z K  wrote:
>>> Other than someone's recollection, there is probably no verifiable means
>>> for determining this information. Sending an inquiry to Martinos Center
>>> Help Desk is your best bet.
>>>
>>> -Zeke
>>>
>>> On 03/31/2015 03:24 PM, Marco Loggia, PhD wrote:
>>>> Hi all,
>>>>
>>>>
>>>> If I wanted to find out what was the 'current' FSL version at the
>>>> Martinos Center on May 1, 2012, how would i do it?
>>>>
>>>> Thanks!
>>>> Marco
>>>> __
>>>>
>>>> Marco L. Loggia, PhD
>>>> Assistant Professor of Radiology
>>>> Harvard Medical School
>>>>
>>>> Massachusetts General Hospital
>>>> 149 Thirteenth Street, Room 2301
>>>> Charlestown, MA 02129
>>>> Phone: (617) 643-7267
>>>> Fax: (617) 726-7422
>>>> Email: ma...@nmr.mgh.harvard.edu <mailto:ma...@nmr.mgh.harvard.edu>
>>>> Web: scholar.harvard.edu/loggia <http://scholar.harvard.edu/loggia>
>>>>
>>>>
>>>>
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>>>
>>>
>>> The information in this e-mail is intended only for the person to whom it is
>>> addressed. If you believe this e-mail was sent to you in error and the 
>>> e-mail
>>> contains patient information, please contact the Partners Compliance 
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you in 
>>> error
>>> but does not contain patient information, please contact the sender and 
>>> properly
>>> dispose of the e-mail.
>>>
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Re: [Freesurfer] 'current' FSL

[dgw]

It may help to provide a bit more context e.g. the email/instructions
you where you found the reference to 'current' fsl version?

HTH,
D

On Tue, Mar 31, 2015 at 3:31 PM, Z K  wrote:
> Other than someone's recollection, there is probably no verifiable means
> for determining this information. Sending an inquiry to Martinos Center
> Help Desk is your best bet.
>
> -Zeke
>
> On 03/31/2015 03:24 PM, Marco Loggia, PhD wrote:
>> Hi all,
>>
>>
>> If I wanted to find out what was the 'current' FSL version at the
>> Martinos Center on May 1, 2012, how would i do it?
>>
>> Thanks!
>> Marco
>> __
>>
>> Marco L. Loggia, PhD
>> Assistant Professor of Radiology
>> Harvard Medical School
>>
>> Massachusetts General Hospital
>> 149 Thirteenth Street, Room 2301
>> Charlestown, MA 02129
>> Phone: (617) 643-7267
>> Fax: (617) 726-7422
>> Email: ma...@nmr.mgh.harvard.edu 
>> Web: scholar.harvard.edu/loggia 
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
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Re: [Freesurfer] Get the 3d coordinate of the center of an ROI

[dgw]

just read in the label of the roi of interest and read in the
respective lh/rh.white (if interested in the white surface) and take
the average of those labels 3d points (note, this will do strange
things: not be on the surface. It may not even be in Brain tissue). If
you then want to be on a vertex just find the point with the minimal
distance from that location (note: that may also do strange things:
for example if the label is the central sulcus you could arbitrarily
end up on one wall or another, which would vary from participant to
participant).

HTH
D

On Fri, Mar 27, 2015 at 5:00 PM, Mads Jensen  wrote:
> Dear list,
>
> I would like to make some plots based on the centerpoint of an ROI, so I
> would like to head if it possible to extract the centerpoint of the ROIs
> from a parcellation (e.g. the Desikan-Killiany Atlas). By the center
> point I mean the 3d coordinate, it is not crucial that it is the center
> it might just be a vertex.
>
> best regards,
> mads
>
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
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[Freesurfer] FS-FAST event length duration

[dgw]

Hi,

How does event length/duration contribute to an FS-FAST analysis. Will
I produce different results, if I specify an event length of 1 second
versus an event length of 0.1 seconds? Most importantly, if yes, how
will they differ?

The reason I am asking is formerly I would use the actual duration of
a button press in my analysis of the  button responses; however, I am
now wondering how appropriate this is.

Thanks,
Dan
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[Freesurfer] fs-fast temporal snr

[dgw]

Hi,

Does FS-FAST perform any temporal SNR calculations on data?

If so, how.

Thanks,
Dan
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[Freesurfer] selxavg3-sess svd NaN error

[dgw]

Hi,

I am having a problem running my selxavg3-sess using Freesurfer 5.3.0
stable. I am getting the following error:

Saving X matrix to
/autofs/cluster/neuromind/dwakeman/mm/subjects/nmr00904/sycabs/sycabs_lh/pr014/Xtmp.mat
Error using svd
Input to SVD must not contain NaN or Inf.

Error in cond (line 36)
s = svd(A);

Error in fast_selxavg3 (line 279)
  XCond = cond(XtX);

>> --
ERROR: fast_selxavg3() failed\n

I have 6 different conditions, and they all appear in all of my par
files (one is attached for example purposes). The NaN's appear in the
range of 13-18 in both the X and y ranges of the Xtmp.mat

What other information do I need to provide to get help debugging my problem.

Thanks,
Dan


sycabs.par
Description: Binary data
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[Freesurfer] viewing question

[dgw]

Hi,

In freeview, when I load a volume the voxels are not square to the
viewing windows. Is there an option to view the data with the voxels
square to the viewing windows?

Thanks,
Dan
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