[Freesurfer] Qdec

[Caroline Beelen]

Dear Freesurfer experts,

I just started using Freesurfer for performing MRI (T1)- group-based ROI 
analysis and managed to go through the first recon-all processing stream and 
making few manual edits. Then I followed first steps of the Qdec -procedure. 
However, there is a separate section on ROI-analysis as well. Are they 
complementary or not (which one to follow best)?
I tried both. However, at the Qdec section I got lost at creating the table: 
how to know volumes of pre-specified structures?
At the ROI-section I got lost at the point of adding labels to the average 
subject:

cd $freesurfer (directory)
mri_label2label \
  --srcsubject avgsubject \
  --srclabel avgsubject/label/lh.BA45.label \
  --trgsubject A06_T1 \
  --trglabel A06_T1/label/lh.BA45.label \
  --hemi lh \
  --regmethod surface
(followed the example)

I got the error of:
subject_dir .../freesurfer
Freesurfer_home .../freesurfer
Loading source lab: 'no such file or directory'...etc. ... ERROR reading 
lh.BA45.label.
What am I doing wrong?

Thank you very much for your response in advance.

Kind regards, Caroline





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Re: [Freesurfer] FW: segmentation fault (core dumped)

[Bruce Fischl]

Hi Fengji

hmmm, I don't remember ever seeing a core dump in mri-segstats before. If 
you upload the entire subject dir (tarred and gzipped) to our ftp site we 
will fix it.


cheers
Bruce


On Mon, 21 Dec 2015, Fengji Geng wrote:


Dear fs experts, 

Could anybody help with the error we reported a week ago?  We tested running 
the same command on the latest version of
freesurfer and the same error msg appeared again. 

Thanks in advance!

---
---

Dear freesurfer developers and users,
I encountered an error as 'segmentation fault (core dumped)' when I run 
'recon-all -all -s $s -hippocampal-subfields-T1T2
$s/T2/*.mgz T1T2'. Attached is the error log. 

The version of freesurfer is 'freesurfer-Linux-centos6_x86_64-dev-20151006'. 

Here goes our server information: 
Distributor ID:RedHatEnterpriseServer
Description:Red Hat Enterprise Linux Server release 6.6 (Santiago)
Release:6.6

Thank you in advance for your help.

- Fengji


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Re: [Freesurfer] missing 3volreg.afni

[Douglas N Greve]

that link works for me. Can you try again?

On 12/20/2015 02:17 AM, Thục Trinh wrote:
> Hi FS experts,
>
> I'm working on my fMRI data using FSFAST v.6 tool. But the first step 
> of Preproc-sess was failed with an error :" *ERROR: cannot find AFNI 
> command 3dvolreg.afni ". *
> I found a thread that had the same error with mine (in FS v.5.3) : 
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg37764.html
>
> But the link to download 3dvolreg.afni doesn't work. Is this the same 
> 3dvolreg.afni for v.5.3 and v.6?
>
> Thanks,
> Trinh
>
>
>
>
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Re: [Freesurfer] Z-score from .label

[Douglas N Greve]

You can use mri_segstats --i z.nii.gz --id 1 --slabel ...

On 12/20/2015 08:44 AM, std...@virgilio.it wrote:
> Hi list,
>
> I would like to extract the mean z-score from a roi.label in each 
> subject after FS-FAST (rs-fMRI seed based).
> How can I do?
>
> Thanks
>
>
> Stefano
>
>
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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
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Re: [Freesurfer] R: R: Re: R: Re: FDR in FS-FAST

[Douglas N Greve]

Try this version for mac
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr.osx

Use mri_surfcluster (or mri_volcluster) to do the clustering


On 12/18/2015 05:11 PM, std...@virgilio.it wrote:
> I have run
> mri_fdr --help
> but I obtained this warning:
> /Applications/freesurfer/bin/mri_fdr: Permission denied.
>
> I would also ask you if is possible to threshold the FDR map (p<0.
> 05),
> eliminating clusters < 5 voxels.
>
> Thanks
>
>
> Stefano
>
>
>
>>> Messaggio originale
>>> Da: gr...@nmr.mgh.harvard.edu
>>> Data: 11-dic-2015 20.23
>>> A: 
>>> Ogg: Re: [Freesurfer] R: Re: FDR in FS-FAST
>>>
>>> $FREESURFER_HOME/bin
>>>
>>> On 12/11/15 2:08 PM, std...@virgilio.it wrote:
 Thanks, in which folder I should put this file?

 Stefano


> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 7-dic-2015 19.23
> A: 
> Ogg: Re: [Freesurfer] FDR in FS-FAST
>
>
>
> On 12/07/2015 08:35 AM, std...@virgilio.it wrote:
>> Hi list,
>> I have two concerns, please:
>> 1) It is possible to apply FDR correction on rs-fMRI seed based
>> analysis by FS-FAST? If yes, I can I do it?
> try this binary
> ftp://surfer.nmr.mgh.harvard.
>> edu/transfer/outgoing/flat/greve/mri_fdr
>> 2) I have apply the FS guidelines and I have used Montecarlo
>> correction with threshold at 1.3 but in the within group
> analysis
 the
>> clusters are very large. In the guide I read examples with a
 threshold
>> at 3. Is there a specific reason?
> There is not a hard-and-fast criteria for the voxel-wise
>> threshold. 3
 is
> fine as is 1.3
>> Thanks
>>
>> Stefano
>>
>>
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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
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 you in error
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 and properly
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>>>
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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
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Re: [Freesurfer] no aseg.stats after recon-all -all?

[Douglas N Greve]

here you go. I put rh there too
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/lh.DKTatlas40.gcs


On 12/18/2015 05:29 PM, Schweren, LJS (med) wrote:
>
> No, it doesn’t exist (lh nor rh)
>
> Can I get it somewhere?
>
> *From:*freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas 
> Greve
> *Sent:* vrijdag 18 december 2015 18:28
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] no aseg.stats after recon-all -all?
>
> Does //usr/local/freesurfer5/average/lh.DKTatlas40.gcs exist?
>
> /
>
> On 12/17/15 5:53 PM, Schweren, LJS (med) wrote:
>
> Dear Freesurfer experts,
>
> I'm trying to get BrainSeg for 5 subjects. I'm running the
> following commands:
>
> /for scan in ...
> do
> cd $SUBJECTS_DIR
> recon-all -all -subjid $scan
> done/
>
> It completes recon-all, but with errors. These are the errors:
>
> /[me@mycomp]$ cat recon-all.error
> --
> SUBJECT [mysubj]
> DATE Thu Dec 17 12:57:00 PST 2015
> USER me
> HOST mycomp
> PROCESSOR x86_64
> OS Linux
> Linux emotion.ucsd.edu 2.6.18-406.el5 #1 SMP Tue Jun 2 17:25:57
> EDT 2015 x86_64 x86_64 x86_64 GNU/Linux
> $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
> /usr/local/freesurfer/bin/recon-all
> PWD /[mypathtoSUBJECTS_DIR]/[mysubj]/scripts
> CMD mris_ca_label -l ../label/lh.cortex.label -aseg
> ../mri/aseg.mgz -seed 1234 [mysubj] lh ../surf/lh.sphere.reg
> /usr/local/freesurfer5/average/lh.DKTatlas40.gcs
> ../label/lh.aparc.DKTatlas40.annot
>
> [me@mycomp]$ cat error.log
> GCSAread(/usr/local/freesurfer5/average/lh.DKTatlas40.gcs): could
> not open file/
>
> As a result, I don't have any aseg.stats, nor any aparc+aseg
> files. I ran mri_segstats separately, but then I only get the
> subcortical volumes, not the totals. If I include the
> --brain-vol-from-seg flag, it errors again, saying:
>
> /$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
> cwd
> cmdline mri_segstats --seg
> /[mypathtoSUBJECTS_DIR]/[mysubj]/mri/aseg.mgz --brain-vol-from-seg
> --ctab /usr/local/freesurfer5/FreeSurferColorLUT.txt --excludeid 0
> --sum /[mypathtoSUBJECTS_DIR]/scripts/[mysubj].aseg.sum
> sysname  Linux
> hostname mycomp
> machine  x86_64
> user me
> UseRobust  0
> Loading /[mypathtoSUBJECTS_DIR]/[mysubj]/mri/aseg.mgz
> Getting Brain Volume Statistics
> MRISread(/[mypathtoSUBJECTS_DIR]/(null)/surf/lh.white): could not
> open file
> No such file or directory
> /
> I'm hoping you can help me! My goal is to get just BrainSeg for
> these subjects, I don't need the other outcomes. So if there is a
> work-around I would be happy to hear. Thank you for your help!
>
> All my best,
> Lizanne
>
> 
>
> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor
> de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen
> gebruik maken van dit bericht, het niet openbaar maken of op enige
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> aansprakelijk gesteld worden voor een incomplete aankomst of
> vertraging van dit verzonden bericht.
>
> The contents of this message are confidential and only intended
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> not allowed to use this message, to make it public or to
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> transferred message.
>
>
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>
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>
> 
> De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de 
> geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik 
> maken van dit bericht, het niet openbaar maken of op enige wijze 
> verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk 
> gesteld worden voor een incomplete aankomst of vertraging van dit 
> verzonden bericht.
>
> The contents of this message are confidential and only intended for 
> the eyes of the addressee(s). Others than the addressee(s) are not 
> allowed to use this message, to make it public or to distribute or 
> multiply this message in any way. The UMCG cannot be held responsible 
> for incomplete reception or delay of this transferred message.
>
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Re: [Freesurfer] Qdec visualization

[Douglas N Greve]

The correction for multiple comparisons is cluster-based. Each cluster 
gets a single number. In the display, all the vertices get that same number.

On 12/18/2015 03:17 PM, John Anderson wrote:
> Hi Freesurfer experts,
> I am using Qdec in Freesurfer 5.3 to do some cortical thickness 
> comparisons between two groups.
>
> Before corrcting the results for multiple comparisons ( monte carlo 
> simulation) the significant differnce between the groups is visualized 
> as a range of color while after correcting  for multiple copmparisons 
> the color of the statistical map is usinform ( Attached)
> Is ther any way to visualze the results as a range of color after 
> correcting the results for multiple comparsiosn
>
> Thanks in advance for any advice
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>
>
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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
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[Freesurfer] Pial Surface, total area?

[Guido Orlando Pascariello]

Hi FS Experts
I want to get the total area from pia cortex, in order to normalize the
parcellations measure. In lh.aparc.statsfile on there is a line:

# Measure Cortex, WhiteSurfArea, White Surface Total Area, ** mm^2
>

I've looking for this topic in the lista and I found there is a way to get
PialSurfArea. However I wonder if needed to achieve my goal. I mean, why
doesn't recon-all measure this area? Is  WhiteSurfArea enought to normalice
the parcellations?

I'll be grateful if you can help
Being all for now, I await a reply

Guido PASCARIELLO
Facultad de Ingeniería - Universidad Nacional de Entre Ríos
Argentina
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[Freesurfer] Hippocampal Subfields on 1.5 Tesla - Freesufer v. 6

[Douglas Merkitch]

Hello Freesurfer experts,

I am wondering if the new hippocampal subfields (HSF) module that will be 
included in Freesurfer v. 6 would work with 1.5 Tesla data.

Upon reviewing the mail archives, I came across a thread 
(https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35665.html) 
regarding the validity of using 1.5 Tesla T1 data with the older HSF module 
from Freesurfer v. 5.3. My takeaway from this thread is that the older module 
should work reasonably well as long as the T1 data is 1mm, regardless of 
whether the data is 1.5 or 3 Tesla (but please correct me if I am wrong!). 
Would the same apply for the new HSF module in Freesurfer v. 6 when it is 
officially released?

Any insight would be greatly appreciated!

Thanks,

Doug

Douglas Merkitch
Neurological Sciences
Rush University Medical Center
Email: douglas_merki...@rush.edu





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Re: [Freesurfer] Fw: Gray matter intensity

[Sabrina Yu]

Hello, 

Thank you for the very helpful replies! I have another quick question. Which 
commands would I use to generate images like the ones  in Figure 1 (C) 
generated in the Salat paper 
(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?

Thank you
Sabrina


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Tuesday, December 15, 2015 10:10 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Gray matter intensity

On 12/15/2015 01:00 PM, Sabrina Yu wrote:
>
> Hi,
>
>
> Just following up on my previous email (see below) as I have not yet
> heard back. I also have another question regarding the lh.wm.mgh and
> rh.wm.mgh generated by pctsurfcon. How do I view these as surface
> overlays on T1 brain scans?
>
If you want to view them on a volume instead of a surface, you can use
mri_surf2vol
>
>
> Thank you very much.
>
>
>
> 
> *From:* Sabrina Yu
> *Sent:* Thursday, December 10, 2015 2:47 PM
> *To:* Freesurfer support list
> *Subject:* Gray matter intensity
>
> Hello,
>
>
>
> I have been following the instructions in this email thread:
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.
> 
>  And
> have successfully gotten the wm-gm signal intensity contrast, but
> now have a few questions regarding signal intensity for white matter
> and gray matter intensity.
>
>
> 1) Does the wmparc.stats contain mean white matter intensity values
> for each ROI?
>
Yes
>
> 2) Is it possible to extract these same mean intensity values for gray
> matter? There is no gmparc.stats file. We know that it's possible to
> calculate these from the WM/GM ratio from pctsurfcon, but it'd be
> great if there was a more direct way to get this data.
>
There is not one by default that includes the cortical parcellation. You
can create your own with mri_segstats passing it the aparc+aseg.mgz as
the segmentation. Look in the recon-all.log file for the command line
that creates the aseg.stats or wmparc.stats. You will probably need to
change the --ctab flag to --ctab-default (no argument)
>
>
> Thank you,
>
> Sabrina Yu
>
>
>
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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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Re: [Freesurfer] Fw: Gray matter intensity

[Douglas N Greve]

freeview or tksurfer. Load the relevant map as an overlay

On 12/21/2015 12:57 PM, Sabrina Yu wrote:
> Hello,
>
> Thank you for the very helpful replies! I have another quick question. Which 
> commands would I use to generate images like the ones  in Figure 1 (C) 
> generated in the Salat paper 
> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
>
> Thank you
> Sabrina
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Tuesday, December 15, 2015 10:10 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>
> On 12/15/2015 01:00 PM, Sabrina Yu wrote:
>> Hi,
>>
>>
>> Just following up on my previous email (see below) as I have not yet
>> heard back. I also have another question regarding the lh.wm.mgh and
>> rh.wm.mgh generated by pctsurfcon. How do I view these as surface
>> overlays on T1 brain scans?
>>
> If you want to view them on a volume instead of a surface, you can use
> mri_surf2vol
>>
>> Thank you very much.
>>
>>
>>
>> 
>> *From:* Sabrina Yu
>> *Sent:* Thursday, December 10, 2015 2:47 PM
>> *To:* Freesurfer support list
>> *Subject:* Gray matter intensity
>>
>> Hello,
>>
>>
>>
>> I have been following the instructions in this email thread:
>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.
>> 
>>  And
>> have successfully gotten the wm-gm signal intensity contrast, but
>> now have a few questions regarding signal intensity for white matter
>> and gray matter intensity.
>>
>>
>> 1) Does the wmparc.stats contain mean white matter intensity values
>> for each ROI?
>>
> Yes
>> 2) Is it possible to extract these same mean intensity values for gray
>> matter? There is no gmparc.stats file. We know that it's possible to
>> calculate these from the WM/GM ratio from pctsurfcon, but it'd be
>> great if there was a more direct way to get this data.
>>
> There is not one by default that includes the cortical parcellation. You
> can create your own with mri_segstats passing it the aparc+aseg.mgz as
> the segmentation. Look in the recon-all.log file for the command line
> that creates the aseg.stats or wmparc.stats. You will probably need to
> change the --ctab flag to --ctab-default (no argument)
>>
>> Thank you,
>>
>> Sabrina Yu
>>
>>
>>
>> ___
>> 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.
>
> ___
> 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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Re: [Freesurfer] Fw: Gray matter intensity

[Sabrina Yu]

When I try to load the overlay in freeview, it crashes immediately. Any 
thoughts on why this happens?

Thanks


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N Greve 

Sent: Monday, December 21, 2015 10:08 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Fw: Gray matter intensity

freeview or tksurfer. Load the relevant map as an overlay

On 12/21/2015 12:57 PM, Sabrina Yu wrote:
> Hello,
>
> Thank you for the very helpful replies! I have another quick question. Which 
> commands would I use to generate images like the ones  in Figure 1 (C) 
> generated in the Salat paper 
> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
>
> Thank you
> Sabrina
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Tuesday, December 15, 2015 10:10 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>
> On 12/15/2015 01:00 PM, Sabrina Yu wrote:
>> Hi,
>>
>>
>> Just following up on my previous email (see below) as I have not yet
>> heard back. I also have another question regarding the lh.wm.mgh and
>> rh.wm.mgh generated by pctsurfcon. How do I view these as surface
>> overlays on T1 brain scans?
>>
> If you want to view them on a volume instead of a surface, you can use
> mri_surf2vol
>>
>> Thank you very much.
>>
>>
>>
>> 
>> *From:* Sabrina Yu
>> *Sent:* Thursday, December 10, 2015 2:47 PM
>> *To:* Freesurfer support list
>> *Subject:* Gray matter intensity
>>
>> Hello,
>>
>>
>>
>> I have been following the instructions in this email thread:
>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.
>> 
>>  And
>> have successfully gotten the wm-gm signal intensity contrast, but
>> now have a few questions regarding signal intensity for white matter
>> and gray matter intensity.
>>
>>
>> 1) Does the wmparc.stats contain mean white matter intensity values
>> for each ROI?
>>
> Yes
>> 2) Is it possible to extract these same mean intensity values for gray
>> matter? There is no gmparc.stats file. We know that it's possible to
>> calculate these from the WM/GM ratio from pctsurfcon, but it'd be
>> great if there was a more direct way to get this data.
>>
> There is not one by default that includes the cortical parcellation. You
> can create your own with mri_segstats passing it the aparc+aseg.mgz as
> the segmentation. Look in the recon-all.log file for the command line
> that creates the aseg.stats or wmparc.stats. You will probably need to
> change the --ctab flag to --ctab-default (no argument)
>>
>> Thank you,
>>
>> Sabrina Yu
>>
>>
>>
>> ___
>> 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.
>
> ___
> 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] R: Re: R: R: Re: R: Re: FDR in FS-FAST

[stdp82]

Thanks but permission denied persist.


>Messaggio originale
>Da: gr...@nmr.mgh.harvard.edu
>Data: 21-dic-2015 17.33
>A: 
>Ogg: Re: [Freesurfer] R: R: Re: R: Re: FDR in FS-FAST
>
>
>Try this version for mac
>ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr.
osx
>
>Use mri_surfcluster (or mri_volcluster) to do the clustering
>
>
>On 12/18/2015 05:11 PM, std...@virgilio.it wrote:
>> I have run
>> mri_fdr --help
>> but I obtained this warning:
>> /Applications/freesurfer/bin/mri_fdr: Permission denied.
>>
>> I would also ask you if is possible to threshold the FDR map (p<0.
>> 05),
>> eliminating clusters < 5 voxels.
>>
>> Thanks
>>
>>
>> Stefano
>>
>>
>>
 Messaggio originale
 Da: gr...@nmr.mgh.harvard.edu
 Data: 11-dic-2015 20.23
 A: 
 Ogg: Re: [Freesurfer] R: Re: FDR in FS-FAST

 $FREESURFER_HOME/bin

 On 12/11/15 2:08 PM, std...@virgilio.it wrote:
> Thanks, in which folder I should put this file?
>
> Stefano
>
>
>> Messaggio originale
>> Da: gr...@nmr.mgh.harvard.edu
>> Data: 7-dic-2015 19.23
>> A: 
>> Ogg: Re: [Freesurfer] FDR in FS-FAST
>>
>>
>>
>> On 12/07/2015 08:35 AM, std...@virgilio.it wrote:
>>> Hi list,
>>> I have two concerns, please:
>>> 1) It is possible to apply FDR correction on rs-fMRI seed 
based
>>> analysis by FS-FAST? If yes, I can I do it?
>> try this binary
>> ftp://surfer.nmr.mgh.harvard.
>>> edu/transfer/outgoing/flat/greve/mri_fdr
>>> 2) I have apply the FS guidelines and I have used Montecarlo
>>> correction with threshold at 1.3 but in the within group
>> analysis
> the
>>> clusters are very large. In the guide I read examples with a
> threshold
>>> at 3. Is there a specific reason?
>> There is not a hard-and-fast criteria for the voxel-wise
>>> threshold. 3
> is
>> fine as is 1.3
>>> Thanks
>>>
>>> Stefano
>>>
>>>
>>> ___
>>> 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.
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>> ___
>> 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
>


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Re: [Freesurfer] R: Re: R: R: Re: R: Re: FDR in FS-FAST

[Douglas N Greve]

have you tried changing the permission to be exectuable?
chmod a+x mri_fdr

On 12/21/2015 02:02 PM, std...@virgilio.it wrote:
> Thanks but permission denied persist.
>
>
>> Messaggio originale
>> Da: gr...@nmr.mgh.harvard.edu
>> Data: 21-dic-2015 17.33
>> A: 
>> Ogg: Re: [Freesurfer] R: R: Re: R: Re: FDR in FS-FAST
>>
>>
>> Try this version for mac
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr.
> osx
>> Use mri_surfcluster (or mri_volcluster) to do the clustering
>>
>>
>> On 12/18/2015 05:11 PM, std...@virgilio.it wrote:
>>> I have run
>>> mri_fdr --help
>>> but I obtained this warning:
>>> /Applications/freesurfer/bin/mri_fdr: Permission denied.
>>>
>>> I would also ask you if is possible to threshold the FDR map (p<0.
>>> 05),
>>> eliminating clusters < 5 voxels.
>>>
>>> Thanks
>>>
>>>
>>> Stefano
>>>
>>>
>>>
> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 11-dic-2015 20.23
> A: 
> Ogg: Re: [Freesurfer] R: Re: FDR in FS-FAST
>
> $FREESURFER_HOME/bin
>
> On 12/11/15 2:08 PM, std...@virgilio.it wrote:
>> Thanks, in which folder I should put this file?
>>
>> Stefano
>>
>>
>>> Messaggio originale
>>> Da: gr...@nmr.mgh.harvard.edu
>>> Data: 7-dic-2015 19.23
>>> A: 
>>> Ogg: Re: [Freesurfer] FDR in FS-FAST
>>>
>>>
>>>
>>> On 12/07/2015 08:35 AM, std...@virgilio.it wrote:
 Hi list,
 I have two concerns, please:
 1) It is possible to apply FDR correction on rs-fMRI seed
> based
 analysis by FS-FAST? If yes, I can I do it?
>>> try this binary
>>> ftp://surfer.nmr.mgh.harvard.
 edu/transfer/outgoing/flat/greve/mri_fdr
 2) I have apply the FS guidelines and I have used Montecarlo
 correction with threshold at 1.3 but in the within group
>>> analysis
>> the
 clusters are very large. In the guide I read examples with a
>> threshold
 at 3. Is there a specific reason?
>>> There is not a hard-and-fast criteria for the voxel-wise
 threshold. 3
>> is
>>> fine as is 1.3
 Thanks

 Stefano


 ___
 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.
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

>>> ___
>>> 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
>>
>
> ___
> Freesurfer 

Re: [Freesurfer] Qdec visualization

[John Anderson]

Thanks you very much Doug,

Please one more question. Is there any way in Qdec to get the stamdard error (SE) ?
 

Bests,
John 

 
 

Sent: Monday, December 21, 2015 at 11:43 AM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec visualization

The correction for multiple comparisons is cluster-based. Each cluster
gets a single number. In the display, all the vertices get that same number.

On 12/18/2015 03:17 PM, John Anderson wrote:
> Hi Freesurfer experts,
> I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> comparisons between two groups.
>
> Before corrcting the results for multiple comparisons ( monte carlo
> simulation) the significant differnce between the groups is visualized
> as a range of color while after correcting for multiple copmparisons
> the color of the statistical map is usinform ( Attached)
> Is ther any way to visualze the results as a range of color after
> correcting the results for multiple comparsiosn
>
> Thanks in advance for any advice
> Bests,
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>
>
> ___
> 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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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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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.

[Freesurfer] R: Re: R: Re: R: R: Re: R: Re: FDR in FS-FAST

[stdp82]

yes and this is the error:
mri_fdr
dyld: Library not loaded: @executable_path/../lib/gcc/lib/libstdc++.6.
dylib
  Referenced from: /Applications/freesurfer/bin/mri_fdr
  Reason: image not found
Trace/BPT trap


>Messaggio originale
>Da: gr...@nmr.mgh.harvard.edu
>Data: 21-dic-2015 20.04
>A: 
>Ogg: Re: [Freesurfer] R: Re: R: R: Re: R: Re: FDR in FS-FAST
>
>have you tried changing the permission to be exectuable?
>chmod a+x mri_fdr
>
>On 12/21/2015 02:02 PM, std...@virgilio.it wrote:
>> Thanks but permission denied persist.
>>
>>
>>> Messaggio originale
>>> Da: gr...@nmr.mgh.harvard.edu
>>> Data: 21-dic-2015 17.33
>>> A: 
>>> Ogg: Re: [Freesurfer] R: R: Re: R: Re: FDR in FS-FAST
>>>
>>>
>>> Try this version for mac
>>> ftp://surfer.nmr.mgh.harvard.
edu/transfer/outgoing/flat/greve/mri_fdr.
>> osx
>>> Use mri_surfcluster (or mri_volcluster) to do the clustering
>>>
>>>
>>> On 12/18/2015 05:11 PM, std...@virgilio.it wrote:
 I have run
 mri_fdr --help
 but I obtained this warning:
 /Applications/freesurfer/bin/mri_fdr: Permission denied.

 I would also ask you if is possible to threshold the FDR map 
(p<0.
 05),
 eliminating clusters < 5 voxels.

 Thanks


 Stefano



>> Messaggio originale
>> Da: gr...@nmr.mgh.harvard.edu
>> Data: 11-dic-2015 20.23
>> A: 
>> Ogg: Re: [Freesurfer] R: Re: FDR in FS-FAST
>>
>> $FREESURFER_HOME/bin
>>
>> On 12/11/15 2:08 PM, std...@virgilio.it wrote:
>>> Thanks, in which folder I should put this file?
>>>
>>> Stefano
>>>
>>>
 Messaggio originale
 Da: gr...@nmr.mgh.harvard.edu
 Data: 7-dic-2015 19.23
 A: 
 Ogg: Re: [Freesurfer] FDR in FS-FAST



 On 12/07/2015 08:35 AM, std...@virgilio.it wrote:
> Hi list,
> I have two concerns, please:
> 1) It is possible to apply FDR correction on rs-fMRI seed
>> based
> analysis by FS-FAST? If yes, I can I do it?
 try this binary
 ftp://surfer.nmr.mgh.harvard.
> edu/transfer/outgoing/flat/greve/mri_fdr
> 2) I have apply the FS guidelines and I have used Montecarlo
> correction with threshold at 1.3 but in the within group
 analysis
>>> the
> clusters are very large. In the guide I read examples with a
>>> threshold
> at 3. Is there a specific reason?
 There is not a hard-and-fast criteria for the voxel-wise
> threshold. 3
>>> is
 fine as is 1.3
> Thanks
>
> Stefano
>
>
> ___
> 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.


>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
 ___
 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

Re: [Freesurfer] Qdec visualization

[Douglas N Greve]

QDEC cannot but the information may be in the output folder. There 
should be a file called gammavar.mgh. This will be the standard variance 
(so take the square root)

On 12/21/2015 02:08 PM, John Anderson wrote:
> Thanks you very much Doug,
> Please one more question. Is there any way in Qdec to get the stamdard 
> error (SE) ?
> Bests,
> John
> *Sent:* Monday, December 21, 2015 at 11:43 AM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec visualization
> The correction for multiple comparisons is cluster-based. Each cluster
> gets a single number. In the display, all the vertices get that same 
> number.
>
> On 12/18/2015 03:17 PM, John Anderson wrote:
> > Hi Freesurfer experts,
> > I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> > comparisons between two groups.
> >
> > Before corrcting the results for multiple comparisons ( monte carlo
> > simulation) the significant differnce between the groups is visualized
> > as a range of color while after correcting for multiple copmparisons
> > the color of the statistical map is usinform ( Attached)
> > Is ther any way to visualze the results as a range of color after
> > correcting the results for multiple comparsiosn
> >
> > Thanks in advance for any advice
> > Bests,
> > John Anderson
> >
> > Senior Research Associate
> > Psychological and Brain Sciences Dept.
> > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > Phone: +1 (603) 646-9834
> > Fax: +1 (603) 646-1419
> >
> >
> > ___
> > 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.
>
>
> ___
> 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

Re: [Freesurfer] FDR in FS-FAST

[Douglas N Greve]

Not sure. Zeke?

On 12/21/2015 02:13 PM, std...@virgilio.it wrote:
> yes and this is the error:
> mri_fdr
> dyld: Library not loaded: @executable_path/../lib/gcc/lib/libstdc++.6.
> dylib
>Referenced from: /Applications/freesurfer/bin/mri_fdr
>Reason: image not found
> Trace/BPT trap
>
>
>> Messaggio originale
>> Da: gr...@nmr.mgh.harvard.edu
>> Data: 21-dic-2015 20.04
>> A: 
>> Ogg: Re: [Freesurfer] R: Re: R: R: Re: R: Re: FDR in FS-FAST
>>
>> have you tried changing the permission to be exectuable?
>> chmod a+x mri_fdr
>>
>> On 12/21/2015 02:02 PM, std...@virgilio.it wrote:
>>> Thanks but permission denied persist.
>>>
>>>
 Messaggio originale
 Da: gr...@nmr.mgh.harvard.edu
 Data: 21-dic-2015 17.33
 A: 
 Ogg: Re: [Freesurfer] R: R: Re: R: Re: FDR in FS-FAST


 Try this version for mac
 ftp://surfer.nmr.mgh.harvard.
> edu/transfer/outgoing/flat/greve/mri_fdr.
>>> osx
 Use mri_surfcluster (or mri_volcluster) to do the clustering


 On 12/18/2015 05:11 PM, std...@virgilio.it wrote:
> I have run
> mri_fdr --help
> but I obtained this warning:
> /Applications/freesurfer/bin/mri_fdr: Permission denied.
>
> I would also ask you if is possible to threshold the FDR map
> (p<0.
> 05),
> eliminating clusters < 5 voxels.
>
> Thanks
>
>
> Stefano
>
>
>
>>> Messaggio originale
>>> Da: gr...@nmr.mgh.harvard.edu
>>> Data: 11-dic-2015 20.23
>>> A: 
>>> Ogg: Re: [Freesurfer] R: Re: FDR in FS-FAST
>>>
>>> $FREESURFER_HOME/bin
>>>
>>> On 12/11/15 2:08 PM, std...@virgilio.it wrote:
 Thanks, in which folder I should put this file?

 Stefano


> Messaggio originale
> Da: gr...@nmr.mgh.harvard.edu
> Data: 7-dic-2015 19.23
> A: 
> Ogg: Re: [Freesurfer] FDR in FS-FAST
>
>
>
> On 12/07/2015 08:35 AM, std...@virgilio.it wrote:
>> Hi list,
>> I have two concerns, please:
>> 1) It is possible to apply FDR correction on rs-fMRI seed
>>> based
>> analysis by FS-FAST? If yes, I can I do it?
> try this binary
> ftp://surfer.nmr.mgh.harvard.
>> edu/transfer/outgoing/flat/greve/mri_fdr
>> 2) I have apply the FS guidelines and I have used Montecarlo
>> correction with threshold at 1.3 but in the within group
> analysis
 the
>> clusters are very large. In the guide I read examples with a
 threshold
>> at 3. Is there a specific reason?
> There is not a hard-and-fast criteria for the voxel-wise
>> threshold. 3
 is
> fine as is 1.3
>> Thanks
>>
>> Stefano
>>
>>
>> ___
>> 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.
>
>
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
> ___
>

Re: [Freesurfer] Qdec visualization

[John Anderson]

Hi Doug,

Given that the  standard variance can be calculated using the command "mris_calc" and the flag "-sqrt" what is the correct command to do this calculation?

I tried: 

mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly what I am doing wrong?

 

 

Bests,
John




Sent: Monday, December 21, 2015 at 2:20 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec visualization

QDEC cannot but the information may be in the output folder. There
should be a file called gammavar.mgh. This will be the standard variance
(so take the square root)

On 12/21/2015 02:08 PM, John Anderson wrote:
> Thanks you very much Doug,
> Please one more question. Is there any way in Qdec to get the stamdard
> error (SE) ?
> Bests,
> John
> *Sent:* Monday, December 21, 2015 at 11:43 AM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec visualization
> The correction for multiple comparisons is cluster-based. Each cluster
> gets a single number. In the display, all the vertices get that same
> number.
>
> On 12/18/2015 03:17 PM, John Anderson wrote:
> > Hi Freesurfer experts,
> > I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> > comparisons between two groups.
> >
> > Before corrcting the results for multiple comparisons ( monte carlo
> > simulation) the significant differnce between the groups is visualized
> > as a range of color while after correcting for multiple copmparisons
> > the color of the statistical map is usinform ( Attached)
> > Is ther any way to visualze the results as a range of color after
> > correcting the results for multiple comparsiosn
> >
> > Thanks in advance for any advice
> > Bests,
> > John Anderson
> >
> > Senior Research Associate
> > Psychological and Brain Sciences Dept.
> > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > Phone: +1 (603) 646-9834
> > Fax: +1 (603) 646-1419
> >
> >
> > ___
> > 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.
>
>
> ___
> 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



___
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] Qdec visualization

[Douglas N Greve]

it helps to see the error  msg, but my guess is that you need to specify 
an mgh file, not a txt file. This will give you the voxel-wise stderr, 
not a standard error for the cluster (which does  not make sense)

On 12/21/2015 02:38 PM, John Anderson wrote:
> Hi Doug,
> Given that the  standard variance can be calculated using the command 
> "mris_calc" and the flag "-sqrt" what is the correct command to do 
> this calculation?
> I tried:
> mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly 
> what I am doing wrong?
> Bests,
> John
> *Sent:* Monday, December 21, 2015 at 2:20 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec visualization
> QDEC cannot but the information may be in the output folder. There
> should be a file called gammavar.mgh. This will be the standard variance
> (so take the square root)
>
> On 12/21/2015 02:08 PM, John Anderson wrote:
> > Thanks you very much Doug,
> > Please one more question. Is there any way in Qdec to get the stamdard
> > error (SE) ?
> > Bests,
> > John
> > *Sent:* Monday, December 21, 2015 at 11:43 AM
> > *From:* "Douglas N Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] Qdec visualization
> > The correction for multiple comparisons is cluster-based. Each cluster
> > gets a single number. In the display, all the vertices get that same
> > number.
> >
> > On 12/18/2015 03:17 PM, John Anderson wrote:
> > > Hi Freesurfer experts,
> > > I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> > > comparisons between two groups.
> > >
> > > Before corrcting the results for multiple comparisons ( monte carlo
> > > simulation) the significant differnce between the groups is visualized
> > > as a range of color while after correcting for multiple copmparisons
> > > the color of the statistical map is usinform ( Attached)
> > > Is ther any way to visualze the results as a range of color after
> > > correcting the results for multiple comparsiosn
> > >
> > > Thanks in advance for any advice
> > > Bests,
> > > John Anderson
> > >
> > > Senior Research Associate
> > > Psychological and Brain Sciences Dept.
> > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > > Phone: +1 (603) 646-9834
> > > Fax: +1 (603) 646-1419
> > >
> > >
> > > ___
> > > 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.
> >
> >
> > ___
> > 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
>
>
> ___
> 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/transf

Re: [Freesurfer] Qdec visualization

[John Anderson]

Thanks Doug,

I used the command "mris_calc gammavar.mgh sqrt" and the output was: "Saving result to 'out.mgz' (type = MGH )"

Then I ran  the command "mris_calc out.mgz stats" and the output was :

         Size                   [ 163842 ]
       Min@(index)        [ 0.00 (161385) ]
      Max@(index)         [ 0.259395 (18208) ]
       Mean                 [ 0.097956 ]
         Std                 [ 0.040943 ]
         Sum             [ 16049.365234 ]
         Prod                 [ 0.00 ]

 

 

In order to calculate the standard error is it fine if I use mris_calc gammavar.mgh stats the I divide the Std of gammavar.mgh by the square root of the sample size ( number of subjects included in the analysis)?

 

 

Thanks a lot!

 

 


 

Sent: Monday, December 21, 2015 at 2:44 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec visualization

it helps to see the error msg, but my guess is that you need to specify
an mgh file, not a txt file. This will give you the voxel-wise stderr,
not a standard error for the cluster (which does not make sense)

On 12/21/2015 02:38 PM, John Anderson wrote:
> Hi Doug,
> Given that the standard variance can be calculated using the command
> "mris_calc" and the flag "-sqrt" what is the correct command to do
> this calculation?
> I tried:
> mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly
> what I am doing wrong?
> Bests,
> John
> *Sent:* Monday, December 21, 2015 at 2:20 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec visualization
> QDEC cannot but the information may be in the output folder. There
> should be a file called gammavar.mgh. This will be the standard variance
> (so take the square root)
>
> On 12/21/2015 02:08 PM, John Anderson wrote:
> > Thanks you very much Doug,
> > Please one more question. Is there any way in Qdec to get the stamdard
> > error (SE) ?
> > Bests,
> > John
> > *Sent:* Monday, December 21, 2015 at 11:43 AM
> > *From:* "Douglas N Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] Qdec visualization
> > The correction for multiple comparisons is cluster-based. Each cluster
> > gets a single number. In the display, all the vertices get that same
> > number.
> >
> > On 12/18/2015 03:17 PM, John Anderson wrote:
> > > Hi Freesurfer experts,
> > > I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> > > comparisons between two groups.
> > >
> > > Before corrcting the results for multiple comparisons ( monte carlo
> > > simulation) the significant differnce between the groups is visualized
> > > as a range of color while after correcting for multiple copmparisons
> > > the color of the statistical map is usinform ( Attached)
> > > Is ther any way to visualze the results as a range of color after
> > > correcting the results for multiple comparsiosn
> > >
> > > Thanks in advance for any advice
> > > Bests,
> > > John Anderson
> > >
> > > Senior Research Associate
> > > Psychological and Brain Sciences Dept.
> > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> > > Phone: +1 (603) 646-9834
> > > Fax: +1 (603) 646-1419
> > >
> > >
> > > ___
> > > 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.
> >
> >
> > ___
> > 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.nm

Re: [Freesurfer] Fw: Gray matter intensity

[Bruce Fischl]

Hi Sabrina

you need to tell us what you did the caused the crash. What was the 
command line? How did you try to load it?

cheers
Bruce
On Mon, 21 Dec 2015, Sabrina Yu 
wrote:

> When I try to load the overlay in freeview, it crashes immediately. Any 
> thoughts on why this happens?
>
> Thanks
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Monday, December 21, 2015 10:08 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>
> freeview or tksurfer. Load the relevant map as an overlay
>
> On 12/21/2015 12:57 PM, Sabrina Yu wrote:
>> Hello,
>>
>> Thank you for the very helpful replies! I have another quick question. Which 
>> commands would I use to generate images like the ones  in Figure 1 (C) 
>> generated in the Salat paper 
>> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
>>
>> Thank you
>> Sabrina
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: Tuesday, December 15, 2015 10:10 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>>
>> On 12/15/2015 01:00 PM, Sabrina Yu wrote:
>>> Hi,
>>>
>>>
>>> Just following up on my previous email (see below) as I have not yet
>>> heard back. I also have another question regarding the lh.wm.mgh and
>>> rh.wm.mgh generated by pctsurfcon. How do I view these as surface
>>> overlays on T1 brain scans?
>>>
>> If you want to view them on a volume instead of a surface, you can use
>> mri_surf2vol
>>>
>>> Thank you very much.
>>>
>>>
>>>
>>> 
>>> *From:* Sabrina Yu
>>> *Sent:* Thursday, December 10, 2015 2:47 PM
>>> *To:* Freesurfer support list
>>> *Subject:* Gray matter intensity
>>>
>>> Hello,
>>>
>>>
>>>
>>> I have been following the instructions in this email thread:
>>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.
>>> 
>>>  And
>>> have successfully gotten the wm-gm signal intensity contrast, but
>>> now have a few questions regarding signal intensity for white matter
>>> and gray matter intensity.
>>>
>>>
>>> 1) Does the wmparc.stats contain mean white matter intensity values
>>> for each ROI?
>>>
>> Yes
>>> 2) Is it possible to extract these same mean intensity values for gray
>>> matter? There is no gmparc.stats file. We know that it's possible to
>>> calculate these from the WM/GM ratio from pctsurfcon, but it'd be
>>> great if there was a more direct way to get this data.
>>>
>> There is not one by default that includes the cortical parcellation. You
>> can create your own with mri_segstats passing it the aparc+aseg.mgz as
>> the segmentation. Look in the recon-all.log file for the command line
>> that creates the aseg.stats or wmparc.stats. You will probably need to
>> change the --ctab flag to --ctab-default (no argument)
>>>
>>> Thank you,
>>>
>>> Sabrina Yu
>>>
>>>
>>>
>>> ___
>>> 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.
>>
>> ___
>> 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:/

[Freesurfer] segmentation fault (core dumped)

[Fengji Geng]

Hi Bruce,

I have uploaded all the data to the server. The command that I run is 
'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'.

It would be great if you could keep us updated on how the fixing is going.

Thanks!

---
Message: 1
Date: Mon, 21 Dec 2015 10:38:08 -0500 (EST)
From: Bruce Fischl 
Subject: Re: [Freesurfer] FW: segmentation fault (core dumped)
To: Freesurfer support list 
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Hi Fengji

hmmm, I don't remember ever seeing a core dump in mri-segstats before. If
you upload the entire subject dir (tarred and gzipped) to our ftp site we
will fix it.

cheers
Bruce



-
Fengji

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The information in this e-mail is intended only for the person to whom it is
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Freesurfer question

[Douglas N Greve]

Sorry for the delay. Answers below

On 12/21/2015 03:58 PM, Woo, Jonghye wrote:
> Dear Doug,
>
> I have following questions: I posted the question but no one answered it.
>
> 1. What is the best way to convert annotation to the segmentation mask 
> (volume)?
mri_label2vol. Specify the annotation with the --annot flag. Run with 
--help to get more help.
>
> 2. I also asked the questions below.
> I tried to use PALS B12 mask in fsaverage, and try to create a volume 
> mask (from the annot file). I used the command below:
> mri_aparc2aseg --s my_subject --annot PALS_B12_Brodmann --o 
> PALS_B12_Brodmann_Mask.nii --annot-table lh_PALS_B12_table.txt
> I’ve got the table from this command: mis_info 
> lh.PALS_B12_Brodmann.annot & mis_info rh.PALS_B12_Brodmann.annot 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/PALS_B12)
> After creating the mask, I compared the table and the mask but they 
> are not corresponding. Rather the labels in the segmentation mask was 
> corresponding to FreeSurferColorLUT.txt.
How are you viewing this? If in tkmedit or freeview, are you specifying 
a color table?
>
> Do you have any suggestions? Thank you in advance.
>
> Best,
> Jonghye
>
>> On Dec 21, 2015, at 11:50 AM, Douglas N Greve 
>> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>>
>> Hi Jonghye, is this something that can be handled over email? Is is 
>> something that cannot be posted to the list?
>> doug
>>
>>
>> On 12/16/2015 11:08 AM, Woo, Jonghye wrote:
>>>
>>> Dear Doug,
>>>
>>> My name is Jonghye and I have a quick question in freesurfer. Can I 
>>> drop by your office for get some information this afternoon? Looking 
>>> forward to hearing from you.
>>>
>>> Best,
>>> Jonghye
>>>
>>>
>>
>> -- 
>> 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/
>>
>

-- 
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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Fw: Gray matter intensity

[Douglas N Greve]

no way to help without more info.

On 12/21/2015 01:10 PM, Sabrina Yu wrote:
> When I try to load the overlay in freeview, it crashes immediately. Any 
> thoughts on why this happens?
>
> Thanks
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> Sent: Monday, December 21, 2015 10:08 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>
> freeview or tksurfer. Load the relevant map as an overlay
>
> On 12/21/2015 12:57 PM, Sabrina Yu wrote:
>> Hello,
>>
>> Thank you for the very helpful replies! I have another quick question. Which 
>> commands would I use to generate images like the ones  in Figure 1 (C) 
>> generated in the Salat paper 
>> (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?
>>
>> Thank you
>> Sabrina
>>
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Douglas N Greve 
>> 
>> Sent: Tuesday, December 15, 2015 10:10 AM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Fw: Gray matter intensity
>>
>> On 12/15/2015 01:00 PM, Sabrina Yu wrote:
>>> Hi,
>>>
>>>
>>> Just following up on my previous email (see below) as I have not yet
>>> heard back. I also have another question regarding the lh.wm.mgh and
>>> rh.wm.mgh generated by pctsurfcon. How do I view these as surface
>>> overlays on T1 brain scans?
>>>
>> If you want to view them on a volume instead of a surface, you can use
>> mri_surf2vol
>>> Thank you very much.
>>>
>>>
>>>
>>> 
>>> *From:* Sabrina Yu
>>> *Sent:* Thursday, December 10, 2015 2:47 PM
>>> *To:* Freesurfer support list
>>> *Subject:* Gray matter intensity
>>>
>>> Hello,
>>>
>>>
>>>
>>> I have been following the instructions in this email thread:
>>> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html.
>>> 
>>>  And
>>> have successfully gotten the wm-gm signal intensity contrast, but
>>> now have a few questions regarding signal intensity for white matter
>>> and gray matter intensity.
>>>
>>>
>>> 1) Does the wmparc.stats contain mean white matter intensity values
>>> for each ROI?
>>>
>> Yes
>>> 2) Is it possible to extract these same mean intensity values for gray
>>> matter? There is no gmparc.stats file. We know that it's possible to
>>> calculate these from the WM/GM ratio from pctsurfcon, but it'd be
>>> great if there was a more direct way to get this data.
>>>
>> There is not one by default that includes the cortical parcellation. You
>> can create your own with mri_segstats passing it the aparc+aseg.mgz as
>> the segmentation. Look in the recon-all.log file for the command line
>> that creates the aseg.stats or wmparc.stats. You will probably need to
>> change the --ctab flag to --ctab-default (no argument)
>>> Thank you,
>>>
>>> Sabrina Yu
>>>
>>>
>>>
>>> ___
>>> 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.
>>
>> ___
>> 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
>
> ___
> Fre

Re: [Freesurfer] Qdec visualization

[Douglas N Greve]

why did you not use fscalc, eg,

fscalc var.mgh -sqrt -o stderr.mgh

On 12/21/2015 03:04 PM, John Anderson wrote:
> Thanks Doug,
> I used the command "mris_calc gammavar.mgh sqrt" and the output was: 
> _"Saving result to 'out.mgz' (type = MGH _)"
> *Then* I ran  the command "mris_calc out.mgz stats" and the output was :
>  Size   [ 163842 ]
>Min@(index)[ 0.00 (161385) ]
>   Max@(index) [ 0.259395 (18208) ]
>Mean [ 0.097956 ]
>  Std [ 0.040943 ]
>  Sum [ 16049.365234 ]
>  Prod [ 0.00 ]
> In order to calculate the standard error is it fine if I use 
> _*mris_calc *__*gammavar.mgh stats*_ the I divide the *Std* of 
> gammavar.mgh by the square root of the sample size ( number of 
> subjects included in the analysis)?
> Thanks a lot!
> *Sent:* Monday, December 21, 2015 at 2:44 PM
> *From:* "Douglas N Greve" 
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Qdec visualization
> it helps to see the error msg, but my guess is that you need to specify
> an mgh file, not a txt file. This will give you the voxel-wise stderr,
> not a standard error for the cluster (which does not make sense)
>
> On 12/21/2015 02:38 PM, John Anderson wrote:
> > Hi Doug,
> > Given that the standard variance can be calculated using the command
> > "mris_calc" and the flag "-sqrt" what is the correct command to do
> > this calculation?
> > I tried:
> > mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly
> > what I am doing wrong?
> > Bests,
> > John
> > *Sent:* Monday, December 21, 2015 at 2:20 PM
> > *From:* "Douglas N Greve" 
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] Qdec visualization
> > QDEC cannot but the information may be in the output folder. There
> > should be a file called gammavar.mgh. This will be the standard variance
> > (so take the square root)
> >
> > On 12/21/2015 02:08 PM, John Anderson wrote:
> > > Thanks you very much Doug,
> > > Please one more question. Is there any way in Qdec to get the stamdard
> > > error (SE) ?
> > > Bests,
> > > John
> > > *Sent:* Monday, December 21, 2015 at 11:43 AM
> > > *From:* "Douglas N Greve" 
> > > *To:* freesurfer@nmr.mgh.harvard.edu
> > > *Subject:* Re: [Freesurfer] Qdec visualization
> > > The correction for multiple comparisons is cluster-based. Each cluster
> > > gets a single number. In the display, all the vertices get that same
> > > number.
> > >
> > > On 12/18/2015 03:17 PM, John Anderson wrote:
> > > > Hi Freesurfer experts,
> > > > I am using Qdec in Freesurfer 5.3 to do some cortical thickness
> > > > comparisons between two groups.
> > > >
> > > > Before corrcting the results for multiple comparisons ( monte carlo
> > > > simulation) the significant differnce between the groups is 
> visualized
> > > > as a range of color while after correcting for multiple copmparisons
> > > > the color of the statistical map is usinform ( Attached)
> > > > Is ther any way to visualze the results as a range of color after
> > > > correcting the results for multiple comparsiosn
> > > >
> > > > Thanks in advance for any advice
> > > > Bests,
> > > > John Anderson
> > > >
> > > > Senior Research Associate
> > > > Psychological and Brain Sciences Dept.
> > > > Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 
> 03755
> > > > Phone: +1 (603) 646-9834
> > > > Fax: +1 (603) 646-1419
> > > >
> > > >
> > > > ___
> > > > 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 

Re: [Freesurfer] Help importing files from a previous SPM analysis

[Luis Fernado Silva Castro de Araújo]

Dear Douglas,

It's an anatomical analysis. Perhaps I misunderstood the requirement for
setting up the directories in the FSFAST for the recon-all command.

If that is the case, it is then a matter of converting my img files into
mgz and run recon-all on them, am I right?

Does the command recon-all also gives me volumes for specific Brodmann's
areas? Or do I have to run a labeling to that?


Thank you,

luis
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Re: [Freesurfer] Help importing files from a previous SPM analysis

[Douglas N Greve]

If you're doing anatomical analysis, then FSFAST is not needed (nor its 
directly structure). If you have an input anatomical volume  in any 
format, then just run

recon-all -s yoursubjectname -all -i inputfile

inputfile can include img but be warned that img does not have 
information about head orientation. This may cause a catastrophic 
failure (eg, the head is upside down). If the head is left-right 
reversed, then it probably won't fail but everything will be left-right 
reversed. don't say I did not warn you:)


On 12/21/2015 05:37 PM, Luis Fernado Silva Castro de Araújo wrote:
>
> Dear Douglas,
>
> It's an anatomical analysis. Perhaps I misunderstood the requirement 
> for setting up the directories in the FSFAST for the recon-all command.
>
> If that is the case, it is then a matter of converting my img files 
> into mgz and run recon-all on them, am I right?
>
> Does the command recon-all also gives me volumes for specific 
> Brodmann's areas? Or do I have to run a labeling to that?
>
>
> Thank you,
>
> luis
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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
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Re: [Freesurfer] segmentation fault (core dumped)

[Douglas N Greve]

what server did you upload it to? What is the name of the file? Make 
sure to include the entire output folder, not just the input files

On 12/21/2015 03:33 PM, Fengji Geng wrote:
> Hi Bruce,
>
> I have uploaded all the data to the server. The command that I run is 
> 'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'.
>
> It would be great if you could keep us updated on how the fixing is 
> going.
>
> Thanks!
>
> ---
> Message: 1
> Date: Mon, 21 Dec 2015 10:38:08 -0500 (EST)
> From: Bruce Fischl 
> Subject: Re: [Freesurfer] FW: segmentation fault (core dumped)
> To: Freesurfer support list 
> Message-ID:
> 
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Fengji
>
> hmmm, I don't remember ever seeing a core dump in mri-segstats before. If
> you upload the entire subject dir (tarred and gzipped) to our ftp site we
> will fix it.
>
> cheers
> Bruce
>
>
>
> -
> Fengji
>
>
>
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-- 
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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
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Re: [Freesurfer] Help importing files from a previous SPM analysis

[Luis Fernado Silva Castro de Araújo]

Do I have to run recon-all entirely in order to extract volume for a few
Brodmann's areas? Or is there a way of optimizing the process by striping
it of any unneeded calculations?

It is taking 21h to analyze one subject.

Best,
luis

2015-12-22 9:44 GMT+11:00 Douglas N Greve :

> If you're doing anatomical analysis, then FSFAST is not needed (nor its
> directly structure). If you have an input anatomical volume  in any
> format, then just run
>
> recon-all -s yoursubjectname -all -i inputfile
>
> inputfile can include img but be warned that img does not have
> information about head orientation. This may cause a catastrophic
> failure (eg, the head is upside down). If the head is left-right
> reversed, then it probably won't fail but everything will be left-right
> reversed. don't say I did not warn you:)
>
>
> On 12/21/2015 05:37 PM, Luis Fernado Silva Castro de Araújo wrote:
> >
> > Dear Douglas,
> >
> > It's an anatomical analysis. Perhaps I misunderstood the requirement
> > for setting up the directories in the FSFAST for the recon-all command.
> >
> > If that is the case, it is then a matter of converting my img files
> > into mgz and run recon-all on them, am I right?
> >
> > Does the command recon-all also gives me volumes for specific
> > Brodmann's areas? Or do I have to run a labeling to that?
> >
> >
> > Thank you,
> >
> > luis
> >
> >
> >
> >
> > ___
> > 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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Re: [Freesurfer] qdec

[Douglas N Greve]

Can you run the command below outside of qdec and send us the error it 
prints to the terminal?

asegstats2table --common-segs --meas volume --tablefile 
/mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
 
--statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 
111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 
117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 
171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 
200109 200614 20 201414 201818 203418 204016 204521 304020 307127 
308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 
412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 
531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 
580044 580347 581349 583858 586460 594156 598568 599671



On 12/14/2015 02:15 PM, levi solomyak wrote:
> Dear experts,
>
> I've been attempting to generate a stats data table in qdec, but each 
> time I get a "Index Error: list index is out of range" error. This is 
> occurring when it is trying to parse the .stats file.
>
>  I've made sure that the files all line up exactly with the qdec table 
> and that SUBJECTS_DIR  is properly sourced so I'm not sure how to fix 
> this problem. Any help would be greatly appreciated!
>
>
> Here are the details of the errors:
>
> 1) machine being used: Linux localhost.localdomain 
> 3.10.0-229.4.2.el7.x86_64 #1 SMP Wed May 13 10:06:09 UTC 2015 x86_64 
> x86_64 x86_64 GNU/Linux
> 2) Freesurfer version: 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0-HCP
> 3) Current working directory: /projects/IndivRITL/data/leviDiff/Subjects
> 4) which qdec :  /usr/local/freesurfer/bin/qdec
> 5) After loading the gui, I attempted to generate a qdec stats table. 
> This is the error that was returned:
>
> ---
> asegstats2table --common-segs --meas volume --tablefile 
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
>  
> --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 
> 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 
> 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 
> 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 
> 200109 200614 20 201414 201818 203418 204016 204521 304020 307127 
> 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 
> 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 
> 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 
> 580044 580347 581349 583858 586460 594156 598568 599671
> SUBJECTS_DIR : /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects
> Parsing the .stats files
> Traceback (most recent call last):
>   File "/usr/local/freesurfer/bin/asegstats2table", line 538, in 
> id_name_map, measurelist = parsed.parse(options.meas)
>   File "/home/usr/local/freesurfer/bin/fsutils.py", line 115, in parse
> self.id_name_map[seg] = strlst[4] # Col 4 is Seg Name
> IndexError: list index out of range
> ERROR: In 
> /usr/pubsw/packages/KWWidgets/CVS-vtk560/KWWidgets/vtkKWTkUtilities.cxx, 
> line 230
> vtkKWQdecApp (0x278d8060):
> Script:
> vtkTemp2 GenerateStatsDataTables
> Returned Error on line 1:
> Uncaught exception: command failed: asegstats2table --common-segs 
> --meas volume --tablefile 
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
>  
> --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 
> 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 
> 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 
> 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 
> 200109 200614 20 201414 201818 203418 204016 204521 304020 307127 
> 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 
> 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 
> 531536 540436 561242 562446 565452 566454 567052 567961 568963 571548 
> 580044 580347 581349 583858 586460 594156 598568 599671
>
> Stack trace:
> Uncaught exception: command failed: asegstats2table --common-segs 
> --meas volume --tablefile 
> /mnt/engram/projects/IndivRITL/data/leviDiff/Subjects/qdec/stats_tables/aseg.volume.stats.dat
>  
> --statsfile=aseg.stats --subjects 100307 101006 104820 105115 110411 
> 111312 111413 111716 112819 113215 113619 113922 114419 115320 116524 
> 117122 117324 118528 135225 135932 150625 150726 151223 151526 170934 
> 171633 172130 172332 172534 172938 173334 175439 177645 177746 178142 
> 200109 200614 20 201414 201818 203418 204016 204521 304020 307127 
> 308331 310621 316633 329440 365343 366042 377451 380036 385450 386250 
> 412528 433839 436239 480141 486759 497865 499566 500222 510326 530635 
> 531536 540436 561242 562446 565452 566454

Re: [Freesurfer] Error in QDEC -"Generate Stats Data Tables"

[Douglas N Greve]

can you cut and paste the error into the email rather than sending a 
jpeg? Your image cut off the most important part

On 12/14/2015 09:54 PM, nellie wrote:
>
> Hi Freesurfer experts,
>
> When I tried to use *"Generate Stats Data Tables*"  in QDEC, some 
> errors came out. The related screenshot is attached in this letter, 
> and I found there wasn't any folder named "pubsw" in the "usr". I 
> wonder how to fix these errors? Thanks a lot.
> Best,
> Amolie
>
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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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
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Re: [Freesurfer] Help importing files from a previous SPM analysis

[Douglas N Greve]

you have to do the whole thing

On 12/21/2015 06:09 PM, Luis Fernado Silva Castro de Araújo wrote:
> Do I have to run recon-all entirely in order to extract volume for a 
> few Brodmann's areas? Or is there a way of optimizing the process by 
> striping it of any unneeded calculations?
>
> It is taking 21h to analyze one subject.
>
> Best,
> luis
>
> 2015-12-22 9:44 GMT+11:00 Douglas N Greve  >:
>
> If you're doing anatomical analysis, then FSFAST is not needed
> (nor its
> directly structure). If you have an input anatomical volume  in any
> format, then just run
>
> recon-all -s yoursubjectname -all -i inputfile
>
> inputfile can include img but be warned that img does not have
> information about head orientation. This may cause a catastrophic
> failure (eg, the head is upside down). If the head is left-right
> reversed, then it probably won't fail but everything will be
> left-right
> reversed. don't say I did not warn you:)
>
>
> On 12/21/2015 05:37 PM, Luis Fernado Silva Castro de Araújo wrote:
> >
> > Dear Douglas,
> >
> > It's an anatomical analysis. Perhaps I misunderstood the requirement
> > for setting up the directories in the FSFAST for the recon-all
> command.
> >
> > If that is the case, it is then a matter of converting my img files
> > into mgz and run recon-all on them, am I right?
> >
> > Does the command recon-all also gives me volumes for specific
> > Brodmann's areas? Or do I have to run a labeling to that?
> >
> >
> > Thank you,
> >
> > luis
> >
> >
> >
> >
> > ___
> > 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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> Freesurfer@nmr.mgh.harvard.edu
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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
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Re: [Freesurfer] Help importing files from a previous SPM analysis

[Bruce Fischl]

Hi Luis

sorry, the BA stuff is almost at the very end so you will need to run 
pretty much everything. We are down to 8 hours or so on modern multi-core 
CPUs (and even faster than that with 4-8 threads)


cheers
Bruce
On Tue, 22 Dec 2015, Luis 
Fernado Silva Castro de Araújo wrote:



Do I have to run recon-all entirely in order to extract volume for a few
Brodmann's areas? Or is there a way of optimizing the process by striping it
of any unneeded calculations?

It is taking 21h to analyze one subject.

Best,
luis

2015-12-22 9:44 GMT+11:00 Douglas N Greve :
  If you're doing anatomical analysis, then FSFAST is not needed
  (nor its
  directly structure). If you have an input anatomical volume  in
  any
  format, then just run

  recon-all -s yoursubjectname -all -i inputfile

  inputfile can include img but be warned that img does not have
  information about head orientation. This may cause a
  catastrophic
  failure (eg, the head is upside down). If the head is left-right
  reversed, then it probably won't fail but everything will be
  left-right
  reversed. don't say I did not warn you:)


  On 12/21/2015 05:37 PM, Luis Fernado Silva Castro de Araújo
  wrote:
  >
  > Dear Douglas,
  >
  > It's an anatomical analysis. Perhaps I misunderstood the
  requirement
  > for setting up the directories in the FSFAST for the recon-all
  command.
  >
  > If that is the case, it is then a matter of converting my img
  files
  > into mgz and run recon-all on them, am I right?
  >
  > Does the command recon-all also gives me volumes for specific
  > Brodmann's areas? Or do I have to run a labeling to that?
  >
  >
  > Thank you,
  >
  > luis
  >
  >
  >
  >
> ___
> 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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e-mail
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HelpLine at
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