Re: [Freesurfer] mri_vol2surf --projopt

[Joerg Pfannmoeller]

The command is:

mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject 
subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii 
--noreshape --cortex

The output is the follwoing:


srcvol = /.../f001.nii
srcreg = /.../register.f001.dof6.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = subjid
surfreg = sphere.reg
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Loading label /.../label/rh.cortex.label
Reading surface /.../surf/rh.white
Done reading source surface
Reading thickness /.../surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
reading gm volume fraction from /.../map001.gm.mgz
reading wm volume fraction from /.../map001.wm.mgz
reading csf volume fraction from /.../map001.csf.mgz
mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject 
subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii 
--noreshape --cortex: Segmentation fault
 
Do you have an idea about the cause of the error?





On Wed, 02 Apr 2014 17:28:14 -0400
Douglas N Greve  wrote:

> what is your command line that is seg faulting? What is the terminal output?
> 
> On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote:
> > Please help me with this issue:
> >
> > If I apply mri_surf2vol to a single volume of unprocessed epi-data, it 
> > results in a segmentation fault. It works if I apply mri_vol2vol for 
> > registration of epi and anatomy, but than an interpolation is 
> > involved. I would like to avoid the interpolation and apply 
> > mri_surf2vol directly to the unprocessed data in order to minimize the 
> > number of interpolations.
> >
> >
> > At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote:
> >
> > This is something BF added Sept 1 2009:
> >
> > added --projopt  switch to do optimal linear estimation of gray matter
> > values given a set of precomputed gray matter densities.
> >
> > I don't know what it would mean beyond that
> >
> > doug
> >
> >
> > On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote:
> > > Hello,
> > >
> > > I found an option in mri_vol2surf for which I could not find a
> > documentation. The option is called:
> > >
> > > --projopt
> > >
> > > It would be nice if somebody could give a description of this
> > option.
> > >
> > > Respectfully yours
> > >
> > > pfannmoe
> > >
> > >
> > > ___
> > > 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


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

Re: [Freesurfer] recon all with 7T data

[falk.luese]

Hi Xiaomin,


you could also try to follow the first few steps of the HiresRecon 
(http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). The parameters of the 
inhomogeneity correction are optimized for 7T data which should help in 
reducing errors due to strong bias fields.


Best,

Falk





Von: Xiaomin Yue
Gesendet: ‎Mittwoch‎, ‎2‎. ‎April‎ ‎2014 ‎15‎:‎23
An: Freesurfer support list





Hi Joe,



Thanks for your response.  For the future reference, it also needs the 
parameter -notal-check, otherwise it will fail again.  Although the 
reconstruction was completed surprisingly without error, a significant amount 
of cortex in the top of the brain was cut off in the brain.mgz file.  It needs 
to be rerun after correcting that error(s).




Xiaomin 


> Date: Tue, 1 Apr 2014 19:52:53 -0400
> From: j...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] recon all with 7T data
> 
> 
> hi Xiaomin,
> 
> 7T data can sometimes cause Talairach failures with the standard
> registration tools due to the strong bias fields. the Talairach
> transformation is used for identifying seed points, and the -use-mritotal
> flag just specifies that the MINC software will be used for the
> Talairach'ing.
> 
> see this page for more info:
> http://freesurfer.net/fswiki/talairach?highlight=%28use%5C-mritotal%29
> 
> 
> -jon
> 
> 
> 
> 
> 
> 
> 
> On Fri, 28 Mar 2014, Xiaomin Yue wrote:
> 
> >
> > I tried to do surfer reconstruction (version 5.3) collected in SIEMENS
> > 7T, with error: imgreg_4dfp
> > /opt/freesurfer-530/average/711-2C_as_mni_average_305
> > /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11
> > none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254.
> > This seems happened for many others. However, the reconstruction worked
> > fine as using data collected from 3T, which means the freesurfer was
> > installed correct, and environment settings are correct as well. Also,
> > the reconstruction on the 7T data can go through using additional
> > parameter: -use-mritotal. My question is how the -use-mritotal
> > parameter would affect final surface?
> > Thanks for providing your input on this.
> > Xiaomin Yue
> >
> ___
> 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


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] Inconsistent results of the same subjects from different Freesurfer processing

[Zixuan Yang]

Dear FreeSurfers,

I have been processing a group of subjects, firstly using Freesurfer V5.1.0 or 
V5.3.0, then V5.3.0 after making some editing on WM and pial surface, using the 
 command, without the <-no-isrunning> option.

I have below message at the beginning of the recon-all after editing:

INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

INFO: SUBJECTS_DIR is /home/zixuan/Work/FS/RE_EDIT
Actual
FREESURFER_HOME /usr/share/freesurfer
-rw-r--r--. 1
zixuan users 957929 Dec 20 16:52 
/home/zixuan/Work/FS/RE_EDIT/D3358/scripts/recon-all.log
Linux NIL.Melbourne 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 
2013 x86_64 x86_64 x86_64 GNU/Linux

INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/share/freesurfer
Previous: /share/apps/freesurfer/5.3.0
#
#@#
Mask BFS Wed Apr  2 17:11:43 EST 2014
/home/zixuan/Work/FS/RE_EDIT/D3358/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz

However all subjects have been finished without error, which is not the case as 
what you have discussed in the mail archive.

recon-all -s  finished without error at Mon Mar 24 03:38:36 EST 2014

The problem is, I found the cortical thickness in regions that I didn't edit 
not consistent before and after re-processing, with about 2-10% differences. 
For some subjects, I have only edited minor pial surface (e.g. entorhinal 
cortex only), yet it seems that all values have been affected.

My question is
1), shall I consider my results valid, despite of the "dismatch" thing? Is 
there any other factors other than editing will affect the final value?

2), I have about 30 subjects processed with V5.1.0, (atrophic brain +++ with 
heavy editing - extreme time consuming), yet I still found some pial to edit 
this time, and processed them with V5.3.0. Shall I consider the values valid 
provided the message "without error", despite the different FreeSurfer versions?

Apologies for cross posting, I didn't found any cases similar to mine in the 
mail archive.

Many thanks and kind regards,
Zixuan


--
Zixuan YANG

Ph.D candidate
Centre for Healthy Brain Ageing (CHeBA)
School of Psychiatry, UNSW Medicine
NPI, Euroa Centre, Barker Street, Randwick
NSW  2031  AUSTRALIA
T: +61 (2) 9385 0427
W: www.cheba.unsw.edu.au
E: z.y...@student.unsw.edu.au
__
Mailing address:
University of New South Wales
Randwick Campus, Building R1f
22-32 King Street, Randwick NSW 2031
Australia

___
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] Create a label from a binary mask

[Cherisse Onuigbo]

Hello

I was wondering how to create a label from a binary mask. I created a mask and 
then normalized it to the template space. When I tried to use mri_cor2vol, all 
the vertex numbers come out as -1. I understand that the vertex numbers should 
come out as -1, but when I entered the coordinates in the display function in 
spm, it was not in the region.

Thank you,
Cherisse___
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] FW: registration difficulty

[Douglas N Greve]

>>should I now rerun the bbregsiter and create a new dat file for the subfield
>> volume to orig.mgz image?

I did not entirely follow this thread. It sound like you have 3 volumes: 
orig.mgz, an EPI, and some highres hippo seg? How did you get the hires hippo 
seg? If it shares a scanner space with the orig.mgz, then run tkregister2 --mov 
hireshippo --s subject --fstarg --reg hip2orig.reg.dat --regheader

this will bring up the tkregister2 window and you can double check that it 
looks ok; save the reg. In the future you can just add --noedit and it will 
write the output reg without bringing up the interface.

but I might not understand what is going on ...
doug

On 04/02/2014 03:03 PM, Erik O'Hanlon wrote:
> Apologies.
>
> forwarded it on now
>
> Thanks a million
>
> Erik
>
> Dr. Erik O'Hanlon PhD MSc BScEng
> Post Doctoral Researcher
>
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie  W: www.rcsi.ie
>
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
> 
> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
> Sent: 02 April 2014 19:58
> To: Erik O'Hanlon
> Subject: Re: [Freesurfer] FW: registration difficulty
>
> Hi Erik
>
> can you cc the list so that others (like Doug!) can respond?
>
> thanks
> Bruce
> On Wed, 2 Apr
> 2014, Erik O'Hanlon wrote:
>
>> Hi Bruce,
>>
>> Thanks so much for your reply. As for the specifics of what I have tried, so
>> rry if it was unclear.
>>
>> I have performed the usual T1 based FS cortical and subcortical analysis and
>>   included the -hip_subfields so I also get all the subdivision volumes. I ha
>> ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo
>> lumes as masks for the purpose of tractography. I created my diff-to-orig da
>> t file using bbregister. I then used this in the mri_vol2vol and aligned my
>> aseg.mgz to my nodif image. This worked really well and I then used fslmaths
>>   to extract out the hippocampus from the aseg2diff. This aligns nicely. I th
>> en tried to apply the same transformation to my subfield volumes but this di
>> dn't work. As you suggested, and just to clarify,
>>
>> should I now rerun the bbregsiter and create a new dat file for the subfield
>>   volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m
>> y subfield volume to the orig.mgz and then run a second mri_vol2vol but use
>> the nodif2orig.dat calculated before and use the nodif image as the --mov fi
>> le and the registered subfield_2orig.nii  as the --targ and use the --inv --
>> nearest settings as I want end up with my subfield volumes in diffusion spac
>> e ?
>>
>> So sorry for the confusion, really shows my lack of experience with FS. Just
>>   getting completely mixed up at this stage.
>>
>> Again apologies for the lack of clarity and confusion but any pointers offer
>> ed would be fantastic.
>>
>> Thanks again
>>
>> best regards
>>
>> Erik
>>
>> __
>>
>> Hi Erik
>>
>> so you had a separate (presumably highres) acquisition within the
>> hippocampus? Have you registered that with bbregister? Your best bet is
>> probably doing so, then composing the two registrations (and inverting one,
>> depending on what direction you want to go).
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
>>
>>>
>>> Dear FS experts,
>>>
>>> I am running my first FS analysis and I'm trying to register my hippocampa
>> l
>>> subdivision volumes to my diffusion space image but cannot get good
>>> alignment. I ran my diffusion preprocessing in ExploreDTI so don't have th
>> e
>>> register.dat file automatically so created this using the bbregister tool
>> and
>>> registered B0 image to my orig.mgz. I then used this dat to align my aseg
>> to
>>> my diffusion space image and it worked well. The issue is when I try to us
>> e
>>> it to transform my hippocampal subfield volumes to diffusion space. They j
>> ust
>>> don't line up. Is this due to the different FOV for the subfields? Can any
>> one
>>> advise how to get these volumes to transform correctly?
>>>
>>> Any help would be greatly appreciated.
>>>
>>> Thanks
>>>
>>> Erik
>> Dr. Erik O'Hanlon PhD MSc BScEng
>> Post Doctoral Researcher
>>
>> [IMAGE]
>>
>> RCSI Psychiatry
>> Royal College of Surgeons in Ireland
>> Beaumont Road, Beaumont, D9, Ireland
>> T: 8093740
>> E: erikohan...@rcsi.ie  W: www.rcsi.ie
>>
>> RCSI DEVELOPING HEALTHCARE LEADERS
>> WHO MAKE A DIFFERENCE WORLDWIDE
>>
>>
>>
>>
>
> 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 

Re: [Freesurfer] FW: registration difficulty

[Douglas N Greve]

If that is the situation, then you can use the --int flag to bbregister

On 04/02/2014 12:19 PM, Bruce Fischl wrote:
> Hi Erik
>
> so you had a separate (presumably highres) acquisition within the
> hippocampus? Have you registered that with bbregister? Your best bet is
> probably doing so, then composing the two registrations (and inverting one,
> depending on what direction you want to go).
>
> cheers
> Bruce
>
>
>
> On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
>
>>
>> Dear FS experts,
>>
>> I am running my first FS analysis and I'm trying to register my hippocampal 
>> subdivision volumes to my diffusion space image but cannot get good 
>> alignment. I ran my diffusion preprocessing in ExploreDTI so don't have the 
>> register.dat file automatically so created this using the bbregister tool 
>> and registered B0 image to my orig.mgz. I then used this dat to align my 
>> aseg to my diffusion space image and it worked well. The issue is when I try 
>> to use it to transform my hippocampal subfield volumes to diffusion space. 
>> They just don't line up. Is this due to the different FOV for the subfields? 
>> Can anyone advise how to get these volumes to transform correctly?
>>
>> Any help would be greatly appreciated.
>>
>> Thanks
>>
>> Erik
>>
>> Dr. Erik O'Hanlon PhD MSc BScEng
>> Post Doctoral Researcher
>>
>>
>> RCSI Psychiatry
>> Royal College of Surgeons in Ireland
>> Beaumont Road, Beaumont, D9, Ireland
>> T: 8093740
>> E: erikohan...@rcsi.ie  W: www.rcsi.ie
>>
>> RCSI DEVELOPING HEALTHCARE LEADERS
>> WHO MAKE A DIFFERENCE WORLDWIDE
>>
>> ___
>> 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


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] mri_vol2surf --projopt

[Douglas N Greve]

what is your command line that is seg faulting? What is the terminal output?

On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote:
> Please help me with this issue:
>
> If I apply mri_surf2vol to a single volume of unprocessed epi-data, it 
> results in a segmentation fault. It works if I apply mri_vol2vol for 
> registration of epi and anatomy, but than an interpolation is 
> involved. I would like to avoid the interpolation and apply 
> mri_surf2vol directly to the unprocessed data in order to minimize the 
> number of interpolations.
>
>
> At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote:
>
> This is something BF added Sept 1 2009:
>
> added --projopt  switch to do optimal linear estimation of gray matter
> values given a set of precomputed gray matter densities.
>
> I don't know what it would mean beyond that
>
> doug
>
>
> On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote:
> > Hello,
> >
> > I found an option in mri_vol2surf for which I could not find a
> documentation. The option is called:
> >
> > --projopt
> >
> > It would be nice if somebody could give a description of this
> option.
> >
> > Respectfully yours
> >
> > pfannmoe
> >
> >
> > ___
> > 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] mri_vol2surf --projopt

[pfannmo...@uni-greifswald.de]

Please help me with this issue:

If I apply mri_surf2vol to a single volume of unprocessed epi-data, it
results in a segmentation fault. It works if I apply mri_vol2vol for
registration of epi and anatomy, but than an interpolation is
involved. I would like to avoid the interpolation and apply
mri_surf2vol directly to the unprocessed data in order to minimize the
number of interpolations.


At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote:


This is something BF added Sept 1 2009:

added --projopt  switch to do optimal linear estimation of gray
matter
values given a set of precomputed gray matter densities.

I don't know what it would mean beyond that

doug


On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote:
> Hello,
>
> I found an option in mri_vol2surf for which I could not find a
documentation. The option is called:
>
> --projopt
>
> It would be nice if somebody could give a description of this
option.
>
> Respectfully yours
>
> pfannmoe
>
>
> ___
> 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


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] mri_vol2surf --projopt

[Douglas N Greve]

This is something BF added Sept 1 2009:

added --projopt  switch to do optimal linear estimation of gray matter
values given a set of precomputed gray matter densities.

I don't know what it would mean beyond that

doug


On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote:
> Hello,
>
> I found an option in mri_vol2surf for which I could not find a documentation. 
> The option is called:
>
> --projopt
>
> It would be nice if somebody could give a description of this option.
>
> Respectfully yours
>
> pfannmoe
>
>
> ___
> 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.

Re: [Freesurfer] FW: registration difficulty

[Erik O'Hanlon]

Apologies.

forwarded it on now

Thanks a million

Erik

Dr. Erik O'Hanlon PhD MSc BScEng
Post Doctoral Researcher


RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie  W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu]
Sent: 02 April 2014 19:58
To: Erik O'Hanlon
Subject: Re: [Freesurfer] FW: registration difficulty

Hi Erik

can you cc the list so that others (like Doug!) can respond?

thanks
Bruce
On Wed, 2 Apr
2014, Erik O'Hanlon wrote:

>
> Hi Bruce,
>
> Thanks so much for your reply. As for the specifics of what I have tried, so
> rry if it was unclear.
>
> I have performed the usual T1 based FS cortical and subcortical analysis and
>  included the -hip_subfields so I also get all the subdivision volumes. I ha
> ve also run a DWI analysis in ExploreDTI and now want to use the subfield vo
> lumes as masks for the purpose of tractography. I created my diff-to-orig da
> t file using bbregister. I then used this in the mri_vol2vol and aligned my
> aseg.mgz to my nodif image. This worked really well and I then used fslmaths
>  to extract out the hippocampus from the aseg2diff. This aligns nicely. I th
> en tried to apply the same transformation to my subfield volumes but this di
> dn't work. As you suggested, and just to clarify,
>
> should I now rerun the bbregsiter and create a new dat file for the subfield
>  volume to orig.mgz image? Do I then use this in the mri_vol2vol and align m
> y subfield volume to the orig.mgz and then run a second mri_vol2vol but use
> the nodif2orig.dat calculated before and use the nodif image as the --mov fi
> le and the registered subfield_2orig.nii  as the --targ and use the --inv --
> nearest settings as I want end up with my subfield volumes in diffusion spac
> e ?
>
> So sorry for the confusion, really shows my lack of experience with FS. Just
>  getting completely mixed up at this stage.
>
> Again apologies for the lack of clarity and confusion but any pointers offer
> ed would be fantastic.
>
> Thanks again
>
> best regards
>
> Erik
>
> __
>
> Hi Erik
>
> so you had a separate (presumably highres) acquisition within the
> hippocampus? Have you registered that with bbregister? Your best bet is
> probably doing so, then composing the two registrations (and inverting one,
> depending on what direction you want to go).
>
> cheers
> Bruce
>
>
>
> On Wed, 2 Apr 2014, Erik O'Hanlon wrote:
>
> >
> >
> > Dear FS experts,
> >
> > I am running my first FS analysis and I'm trying to register my hippocampa
> l
> > subdivision volumes to my diffusion space image but cannot get good
> > alignment. I ran my diffusion preprocessing in ExploreDTI so don't have th
> e
> > register.dat file automatically so created this using the bbregister tool
> and
> > registered B0 image to my orig.mgz. I then used this dat to align my aseg
> to
> > my diffusion space image and it worked well. The issue is when I try to us
> e
> > it to transform my hippocampal subfield volumes to diffusion space. They j
> ust
> > don't line up. Is this due to the different FOV for the subfields? Can any
> one
> > advise how to get these volumes to transform correctly?
> >
> > Any help would be greatly appreciated.
> >
> > Thanks
> >
> > Erik
>
> Dr. Erik O'Hanlon PhD MSc BScEng
> Post Doctoral Researcher
>
> [IMAGE]
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie  W: www.rcsi.ie
>
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
>
>
>
>


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

Re: [Freesurfer] Displaying parcellated ROI in color but remainder of brain in grey

[Laura Taylor]

Hi Doug,

Thank you for your reply.

This was my mris_label2annot command line:

woodward@Bambi:~$ mris_label2annot --s TGT_N61AvgSubject --h rh --ctab
/Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
--a Comp2RH_TGTN61_properGreyRH --l
/Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label
--l
/Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label
--l
/Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label
--l
/Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label
--l
/Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label
--l
/Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label




This is the terminal output:

Reading ctab
/Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
Number of ctab entries 76

$Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $
cwd /home/woodward
cmdline mris_label2annot --s TGT_N61AvgSubject --h rh --ctab
/Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
--a Comp2RH_TGTN61_properGreyRH --l
/Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_collat_transv_ant.label
--l
/Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_oc-temp_med_and_Lingual.label
--l
/Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_med-Lingual.label
--l
/Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.G_oc-temp_lat-fusifor.label
--l
/Data/freesurfer/subjects//TGT_N61AvgSubject/mri_annotation2label/rh.S_occipital_ant.label
--l
/Data/freesurfer/subjects/TGT_N61AvgSubject/mri_annotation2label/rh.S_temporal_inf.label

sysname  Linux
hostname Bambi
machine  x86_64
user woodward

subject TGT_N61AvgSubject
hemirh
SUBJECTS_DIR /Data/freesurfer/subjects
ColorTable
/Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab
AnnotName  Comp2RH_TGTN61_properGreyRH
nlables 6
LabelThresh 0 0.00
Loading /Data/freesurfer/subjects/TGT_N61AvgSubject/surf/rh.orig
 1 8355711 G_and_S_frontomargin
 2 8355711 G_and_S_occipital_inf
 3 8355711 G_and_S_paracentral
 4 8355711 G_and_S_subcentral
 5 8355711 G_and_S_transv_frontopol
 6 8355711 G_and_S_cingul-Ant
Mapping unhit to unknown
Found 154540 unhit vertices
Writing annot to
/Data/freesurfer/subjects/TGT_N61AvgSubject/label/rh.Comp2RH_TGTN61_properGreyRH.annot




colortab file:
/Data/freesurfer/subjects/TGT_N61AvgSubject/label/aparc.annot.a2009s_comp2RH.ctab

 0  Unknown   0   0   00
  1  G_and_S_frontomargin 127 127 127   0
  2  G_and_S_occipital_inf127 127 127   0
  3  G_and_S_paracentral  127 127 127   0
  4  G_and_S_subcentral   127 127 127   0
  5  G_and_S_transv_frontopol 127 127 127   0
  6  G_and_S_cingul-Ant   127 127 127   0
  7  G_and_S_cingul-Mid-Ant   127 127 127   0
  8  G_and_S_cingul-Mid-Post  127 127 127   0
  9  G_cingul-Post-dorsal 127 127 127   0
 10  G_cingul-Post-ventral127 127 127   0
 11  G_cuneus 127 127 127   0
 12  G_front_inf-Opercular127 127 127   0
 13  G_front_inf-Orbital  127 127 127   0
 14  G_front_inf-Triangul 127 127 127   0
 15  G_front_middle   127 127 127   0
 16  G_front_sup  127 127 127   0
 17  G_Ins_lg_and_S_cent_ins  127 127 127   0
 18  G_insular_short  127 127 127   0
 19  G_occipital_middle   127 127 127   0
 20  G_occipital_sup  127 127 127   0
 21  G_oc-temp_lat-fusifor60  20 1400
 22  G_oc-temp_med-Lingual   220 180 1400
 23  G_oc-temp_med-Parahip127 127 127   0
 24  G_orbital127 127 127   0
 25  G_pariet_inf-Angular 127 127 127   0
 26  G_pariet_inf-Supramar127 127 127   0
 27  G_parietal_sup   127 127 127   0
 28  G_postcentral127 127 127   0
 29  G_precentral 127 127 127   0
 30  G_precuneus  127 127 127   0
 31  G_rectus 127 127 127   0
 32  G_subcallosal127 127 127   0
 33  G_temp_sup-G_T_transv127 127 127   0
 34  G_temp_sup-Lateral   127 127 127   0
 35  G_temp_sup-Plan_polar127 127 127   0
 36  G_temp_sup-Plan_tempo127 127 127   0
 37  G_temporal_inf   127 127 127   0
 38  G_temporal_middle127 127 127   0
 39  Lat_Fis-ant-Horizont 127 127 127   0
 40  Lat_Fis-ant-Vertical 127 127 127   0
 41  Lat_Fis-post 127 127 127   0
 42  Medial_wall  127 127 127 

Re: [Freesurfer] quality T1 scans for new study

[Kok, JG (neuro)]

Great, thanks again!


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Verzonden: woensdag 2 april 2014 18:22
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

sure, that would be fine. Upload teh whole dataset and we will take a
look
Bruce
On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:

> Hi Bruce,
>
> Thank you very much for your time. I was just talking to our physicist on 
> this subject, and he said, as you judge the quality of a sequence by its 
> parameters, it may make more sense to run a scan using the parameters as 
> proposed by Freesurfer for Philips (as in the body of the email yesterday) 
> than to ask you to comment on our parameters.
>
> As I agree that may be more sensible, we will try that first. Thank you very 
> much for your considerations (so far)!
>
> Cheers,
>
> Jelmer
>
>
>
> 
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Verzonden: woensdag 2 april 2014 14:30
> Aan: Freesurfer support list
> CC: Andre van der Kouwe
> Onderwerp: Re: [Freesurfer] quality T1 scans for new study
>
> Hi Jelmer
>
> I took a quick look, but it is a lot easier for us if you extract the
> relevant parameters, as we are not that familiar with Philips in general.
> Is this inversion-prepared? I didn't see a TI. Generally
> inversion-preparation improves T1 CNR/unit-time. Also, your wrap direction
> looks like it is A/P.You might try making it L/R instead which is a shorter
> dimension. What coil are you using? Are you using sense?
>
> cheers
> Bruce
>
>
> On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:
>
>> Dear Bruce, Andre, someone else,
>>
>> I think I caused some misunderstanding yesterday for which I am sorry. Now I 
>> do not know on what parameters Andre commented. So to hopefully make things 
>> clear I am once more attaching the parameter file which was used to create a 
>> T1 image (see attached screenshots) that may be of good quality. I hope you 
>> are willing to have a look and see if these parameters would result in good 
>> quaity T1 images.
>>
>> Thanks,
>>
>> Jelmer
>>
>>
>> 
>> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) 
>> [j.g.ko...@umcg.nl]
>> Verzonden: dinsdag 1 april 2014 18:17
>> Aan: Freesurfer support list
>> Onderwerp: Re: [Freesurfer] quality T1 scans for new study
>>
>> Hi Andre,
>>
>> I hope you looked at the attached "scan1_parameter_file.txt" when you 
>> mentioned that you think it seemed to be a reasonable protocol: the 
>> parameters in the body of the email Bruce is referring to were the suggested 
>> parameters in 
>> "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf";,
>>  not the ones I am using/planning to adjust.
>>
>> Thanks,
>>
>> Jelmer
>>
>>
>> 
>> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
>> [fis...@nmr.mgh.harvard.edu]
>> Verzonden: dinsdag 1 april 2014 18:10
>> Aan: Freesurfer support list
>> CC: Andre van der Kouwe
>> Onderwerp: Re: [Freesurfer] quality T1 scans for new study
>>
>> no, I just looked at the ones in the body of your email
>> On Tue, 1 Apr 2014,
>> Kok, JG (neuro) wrote:
>>
>>> Dear Bruce and Andre,
>>>
>>> PS I am sorry, but may I assume you have only looked at the parameters in 
>>> "scan1_parameter_file.txt" and not in
>>> "scan2_parameter_file.txt"? That would be fine, but I would just like to 
>>> check we are talking about the same scan parameters
>>> that seem to be fine...
>>>
>>> Thanks,
>>>
>>> Jelmer
>>>
>>> 
>>> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) 
>>> [j.g.ko...@umcg.nl]
>>> Verzonden: dinsdag 1 april 2014 16:45
>>> Aan: Freesurfer support list
>>> Onderwerp: Re: [Freesurfer] quality T1 scans for new study
>>>
>>> Hi Bruce and Andre,
>>>
>>> Many thanks for your comments!
>>>
>>> Cheers,
>>>
>>> Jelmer
>>>
>>> 
>>> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
>>> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Andre van der Kouwe
>>> [an...@nmr.mgh.harvard.edu]
>>> Verzonden: dinsdag 1 april 2014 15:37
>>> Aan: Bruce Fischl; Freesurfer support list
>>> Onderwerp: Re: [Freesurfer] quality T1 scans for new study
>>>
>>> No, I think that's a reasonable protocol to use and good to use SENSE to 
>>> speed it up.
>>>
>>>  Original message 
>>> From: Bruce

Re: [Freesurfer] quality T1 scans for new study

[Bruce Fischl]

sure, that would be fine. Upload teh whole dataset and we will take a 
look

Bruce
On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:


Hi Bruce,

Thank you very much for your time. I was just talking to our physicist on this 
subject, and he said, as you judge the quality of a sequence by its parameters, 
it may make more sense to run a scan using the parameters as proposed by 
Freesurfer for Philips (as in the body of the email yesterday) than to ask you 
to comment on our parameters.

As I agree that may be more sensible, we will try that first. Thank you very 
much for your considerations (so far)!

Cheers,

Jelmer




Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Verzonden: woensdag 2 april 2014 14:30
Aan: Freesurfer support list
CC: Andre van der Kouwe
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

Hi Jelmer

I took a quick look, but it is a lot easier for us if you extract the
relevant parameters, as we are not that familiar with Philips in general.
Is this inversion-prepared? I didn't see a TI. Generally
inversion-preparation improves T1 CNR/unit-time. Also, your wrap direction
looks like it is A/P.You might try making it L/R instead which is a shorter
dimension. What coil are you using? Are you using sense?

cheers
Bruce


On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:


Dear Bruce, Andre, someone else,

I think I caused some misunderstanding yesterday for which I am sorry. Now I do 
not know on what parameters Andre commented. So to hopefully make things clear 
I am once more attaching the parameter file which was used to create a T1 image 
(see attached screenshots) that may be of good quality. I hope you are willing 
to have a look and see if these parameters would result in good quaity T1 
images.

Thanks,

Jelmer



Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) 
[j.g.ko...@umcg.nl]
Verzonden: dinsdag 1 april 2014 18:17
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

Hi Andre,

I hope you looked at the attached "scan1_parameter_file.txt" when you mentioned that you 
think it seemed to be a reasonable protocol: the parameters in the body of the email Bruce is 
referring to were the suggested parameters in 
"http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf";, 
not the ones I am using/planning to adjust.

Thanks,

Jelmer



Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 18:10
Aan: Freesurfer support list
CC: Andre van der Kouwe
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

no, I just looked at the ones in the body of your email
On Tue, 1 Apr 2014,
Kok, JG (neuro) wrote:


Dear Bruce and Andre,

PS I am sorry, but may I assume you have only looked at the parameters in 
"scan1_parameter_file.txt" and not in
"scan2_parameter_file.txt"? That would be fine, but I would just like to check 
we are talking about the same scan parameters
that seem to be fine...

Thanks,

Jelmer


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) 
[j.g.ko...@umcg.nl]
Verzonden: dinsdag 1 april 2014 16:45
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

Hi Bruce and Andre,

Many thanks for your comments!

Cheers,

Jelmer


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Andre van der Kouwe
[an...@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 15:37
Aan: Bruce Fischl; Freesurfer support list
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

No, I think that's a reasonable protocol to use and good to use SENSE to speed 
it up.

 Original message 
From: Bruce Fischl
Date:04/01/2014 2:28 PM (GMT+02:00)
To: Freesurfer support list
Cc: Andre van der Kouwe
Subject: Re: [Freesurfer] quality T1 scans for new study

looks pretty reasonable. Andre: any comments/suggestions?

On Tue, 1 Apr
2014, Kok, JG (neuro) wrote:


Hi Bruce,

Thanks for your fast reply.

Hereby I attach the parameter files of both scans (although I suspect looking at the 
parameters of "scan1" may be sufficient).

Checking it with the information on Philips at
"http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf":


"
Sequence: T1W_3D_TFE_SENSE
Acquisition time: 5:13
Voxel size: 1.0 x 1.0 x 1.0 mm3
Geometry: FoV 256 mm (256 x 2

Re: [Freesurfer] FW: registration difficulty

[Bruce Fischl]

Hi Erik

so you had a separate (presumably highres) acquisition within the 
hippocampus? Have you registered that with bbregister? Your best bet is 
probably doing so, then composing the two registrations (and inverting one, 
depending on what direction you want to go).

cheers
Bruce



On Wed, 2 Apr 2014, Erik O'Hanlon wrote:

>
>
> Dear FS experts,
>
> I am running my first FS analysis and I'm trying to register my hippocampal 
> subdivision volumes to my diffusion space image but cannot get good 
> alignment. I ran my diffusion preprocessing in ExploreDTI so don't have the 
> register.dat file automatically so created this using the bbregister tool and 
> registered B0 image to my orig.mgz. I then used this dat to align my aseg to 
> my diffusion space image and it worked well. The issue is when I try to use 
> it to transform my hippocampal subfield volumes to diffusion space. They just 
> don't line up. Is this due to the different FOV for the subfields? Can anyone 
> advise how to get these volumes to transform correctly?
>
> Any help would be greatly appreciated.
>
> Thanks
>
> Erik
>
> Dr. Erik O'Hanlon PhD MSc BScEng
> Post Doctoral Researcher
>
>
> RCSI Psychiatry
> Royal College of Surgeons in Ireland
> Beaumont Road, Beaumont, D9, Ireland
> T: 8093740
> E: erikohan...@rcsi.ie  W: www.rcsi.ie
>
> RCSI DEVELOPING HEALTHCARE LEADERS
> WHO MAKE A DIFFERENCE WORLDWIDE
>
> ___
> 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] quality T1 scans for new study

[Kok, JG (neuro)]

Hi Bruce,

Thank you very much for your time. I was just talking to our physicist on this 
subject, and he said, as you judge the quality of a sequence by its parameters, 
it may make more sense to run a scan using the parameters as proposed by 
Freesurfer for Philips (as in the body of the email yesterday) than to ask you 
to comment on our parameters.

As I agree that may be more sensible, we will try that first. Thank you very 
much for your considerations (so far)!

Cheers,

Jelmer




Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Verzonden: woensdag 2 april 2014 14:30
Aan: Freesurfer support list
CC: Andre van der Kouwe
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

Hi Jelmer

I took a quick look, but it is a lot easier for us if you extract the
relevant parameters, as we are not that familiar with Philips in general.
Is this inversion-prepared? I didn't see a TI. Generally
inversion-preparation improves T1 CNR/unit-time. Also, your wrap direction
looks like it is A/P.You might try making it L/R instead which is a shorter
dimension. What coil are you using? Are you using sense?

cheers
Bruce


On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:

> Dear Bruce, Andre, someone else,
>
> I think I caused some misunderstanding yesterday for which I am sorry. Now I 
> do not know on what parameters Andre commented. So to hopefully make things 
> clear I am once more attaching the parameter file which was used to create a 
> T1 image (see attached screenshots) that may be of good quality. I hope you 
> are willing to have a look and see if these parameters would result in good 
> quaity T1 images.
>
> Thanks,
>
> Jelmer
>
>
> 
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) 
> [j.g.ko...@umcg.nl]
> Verzonden: dinsdag 1 april 2014 18:17
> Aan: Freesurfer support list
> Onderwerp: Re: [Freesurfer] quality T1 scans for new study
>
> Hi Andre,
>
> I hope you looked at the attached "scan1_parameter_file.txt" when you 
> mentioned that you think it seemed to be a reasonable protocol: the 
> parameters in the body of the email Bruce is referring to were the suggested 
> parameters in 
> "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf";,
>  not the ones I am using/planning to adjust.
>
> Thanks,
>
> Jelmer
>
>
> 
> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
> [fis...@nmr.mgh.harvard.edu]
> Verzonden: dinsdag 1 april 2014 18:10
> Aan: Freesurfer support list
> CC: Andre van der Kouwe
> Onderwerp: Re: [Freesurfer] quality T1 scans for new study
>
> no, I just looked at the ones in the body of your email
> On Tue, 1 Apr 2014,
> Kok, JG (neuro) wrote:
>
>> Dear Bruce and Andre,
>>
>> PS I am sorry, but may I assume you have only looked at the parameters in 
>> "scan1_parameter_file.txt" and not in
>> "scan2_parameter_file.txt"? That would be fine, but I would just like to 
>> check we are talking about the same scan parameters
>> that seem to be fine...
>>
>> Thanks,
>>
>> Jelmer
>>
>> 
>> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) 
>> [j.g.ko...@umcg.nl]
>> Verzonden: dinsdag 1 april 2014 16:45
>> Aan: Freesurfer support list
>> Onderwerp: Re: [Freesurfer] quality T1 scans for new study
>>
>> Hi Bruce and Andre,
>>
>> Many thanks for your comments!
>>
>> Cheers,
>>
>> Jelmer
>>
>> 
>> Van: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] namens Andre van der Kouwe
>> [an...@nmr.mgh.harvard.edu]
>> Verzonden: dinsdag 1 april 2014 15:37
>> Aan: Bruce Fischl; Freesurfer support list
>> Onderwerp: Re: [Freesurfer] quality T1 scans for new study
>>
>> No, I think that's a reasonable protocol to use and good to use SENSE to 
>> speed it up.
>>
>>  Original message 
>> From: Bruce Fischl
>> Date:04/01/2014 2:28 PM (GMT+02:00)
>> To: Freesurfer support list
>> Cc: Andre van der Kouwe
>> Subject: Re: [Freesurfer] quality T1 scans for new study
>>
>> looks pretty reasonable. Andre: any comments/suggestions?
>>
>> On Tue, 1 Apr
>> 2014, Kok, JG (neuro) wrote:
>>
>>> Hi Bruce,
>>>
>>> Thanks for your fast reply.
>>>
>>> Hereby I attach the parameter files of both scans (although I suspect 
>>> looking at the parameters of "scan1" may be sufficient).
>> Checking it with the information on Philips at
>> "http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.

[Freesurfer] FW: registration difficulty

[Erik O'Hanlon]

Dear FS experts,

I am running my first FS analysis and I'm trying to register my hippocampal 
subdivision volumes to my diffusion space image but cannot get good alignment. 
I ran my diffusion preprocessing in ExploreDTI so don't have the register.dat 
file automatically so created this using the bbregister tool and registered B0 
image to my orig.mgz. I then used this dat to align my aseg to my diffusion 
space image and it worked well. The issue is when I try to use it to transform 
my hippocampal subfield volumes to diffusion space. They just don't line up. Is 
this due to the different FOV for the subfields? Can anyone advise how to get 
these volumes to transform correctly?

Any help would be greatly appreciated.

Thanks

Erik

Dr. Erik O'Hanlon PhD MSc BScEng
Post Doctoral Researcher


RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie  W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE

___
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] mri_vol2surf --projopt

[Joerg Pfannmoeller]

Hello,

I found an option in mri_vol2surf for which I could not find a documentation. 
The option is called:

   --projopt

It would be nice if somebody could give a description of this option.

Respectfully yours

   pfannmoe


___
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] preprocessing question

[Douglas N Greve]

a couple of thiings to check: make sure it is exectuable and make sure 
that you rehash your path. Make sure that if you type fslmaths.fsl that 
it runs something

On 04/02/2014 03:23 AM, Eiran Harel wrote:
> Thanks Doug, i downloaded it and now the file exists:
>
> $FREESURFER_HOME/bin/fslmaths.fsl
>
> Unfortuantely it is still not running and gives the same error when running 
> preproc-sess:
>
> mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 
> -nerode 0
> ERROR: cannot find either fslmaths for avwmaths
>
> How can i proceed?
> Thanks,
> Eiran
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, April 02, 2014 12:41 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] preprocessing question
>
> thanks, it must be something in our distribution script affecting mac
>
> On 04/01/2014 05:13 PM, Markus Gschwind wrote:
>> Thanks Doug,
>>
>> I notice that on my Mac
>> build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>>
>> ...I don't have fslmaths.fsl neither. There are only
>>
>>  $ which $FREESURFER_HOME/bin/fsl*
>>  /Applications/freesurfer/bin/fsl_label2voxel
>>  /Applications/freesurfer/bin/fsl_rigid_register
>>  /Applications/freesurfer/bin/fsl_sub_mgh
>>  /Applications/freesurfer/bin/fslregister
>>
>>  $ which $FREESURFER_HOME/bin/*.fsl
>>  /Applications/freesurfer/bin/epidewarp.fsl
>>  /Applications/freesurfer/bin/fscalc.fsl
>>  /Applications/freesurfer/bin/mri_motion_correct.fsl
>>
>> (I never executed the above mentioned process of Eiran thoug...)
>>
>> Best,
>> Markus
>>
>>
>>
>>
>>
>> 2014-04-01 18:36 GMT+02:00 Douglas N Greve > >:
>>
>>  That is weird. You can get a copy from here
>>
>>  
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac
>>
>>  copy it to
>>
>>  $FREESURFER_HOME/bin/fslmaths.fsl
>>
>>
>>  On 04/01/2014 12:25 PM, Eiran Harel wrote:
>>  > Hi Doug,
>>  > No, it does not exist.
>>  > What should i do?
>>  > Thanks,
>>  > Eiran
>>  > 
>>  > From: freesurfer-boun...@nmr.mgh.harvard.edu
>>  
>>  [freesurfer-boun...@nmr.mgh.harvard.edu
>>  ] on behalf of
>>  Douglas N Greve [gr...@nmr.mgh.harvard.edu
>>  ]
>>  > Sent: Tuesday, April 01, 2014 7:16 PM
>>  > To: freesurfer@nmr.mgh.harvard.edu
>>  
>>  > Subject: Re: [Freesurfer] preprocessing question
>>  >
>>  > does $FREESURFER_HOME/bin/fslmaths.fsl exist?
>>  >
>>  > On 04/01/2014 03:59 AM, Eiran Harel wrote:
>>  >> Dear freesurfers,
>>  >> I have installed freesurfer and fsl on my Mac:
>>  >> *
>>  >> *
>>  >> * freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>>  *
>>  >> *Setting up environment for FreeSurfer/FS-FAST (and FSL)*
>>  >> *FREESURFER_HOME   /Applications/freesurfer*
>>  >> *FSFAST_HOME /Applications/freesurfer/fsfast*
>>  >> *FSF_OUTPUT_FORMAT nii.gz*
>>  >> *SUBJECTS_DIR  /Applications/freesurfer/subjects*
>>  >> *MNI_DIR /Applications/freesurfer/mni*
>>  >> *FSL_DIR   /usr/local/fsl*
>>  >>
>>  >> I am trying to run Preproc-sess command:
>>  >>
>>  >> *preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm
>>  5 -fsd
>>  >> bold -stc odd -per-run -force*
>>  >>
>>  >> and get this error:
>>  >>
>>  >> *mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1
>>  >> -ndil 1 -nerode 0*
>>  >> *ERROR: cannot find either fslmaths for avwmaths*
>>  >> *
>>  >> *
>>  >> Any suggestions?
>>  >> Thanks!
>>  >> Eiran
>>  >>
>>  >>
>>  >>
>>  >>
>>  >> 
>>  >> 
>>  >>    
>>  >> 
>>  >>
>>  >>
>>  >>
>>  >>
>>  >> ___
>>  >> 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
>>  
>>  > FileDro

Re: [Freesurfer] mris_make_face_parcellation

[Karen Marie Sandø Ambrosen]

Hi Bruce,

How can I remove the non-cortical parcels from the annotation file 
created by mris_make_face_parcellation, such that I obtain an annotation 
file with approx. the same number of parcels as ?h.aparc.annot.


Best,
Karen

On 04/01/2014 02:05 PM, Bruce Fischl wrote:

Hi Karen

sorry, I don't think so. You could certainly discard parcels that have 
a substantial non-cortical component to them, but parcellating the 
remainder of the surface uniformly isn't trivial.


cheers
Bruce
On Tue, 1 Apr 2014, Karen Marie Sandø Ambrosen wrote:


Hi Freesurfer experts,

I first parcellated the ?h.aparc.annot using the
mris_divide_parcellation and at first glance it seems fine. However, I
experienced that the size of the regions varies a lot. I then found the
mris_make_face_parcellation, that parcellate the surface in regions of
more equal sizes. Unfortunately the mris_make_face_parcallation uses the
whole surface including the medial wall. Is there any way I can get rid
of the labels covering the medial wall and obtain a parcellation with
the same number of vertices as ?h.apac.annot, but with regions of equal
size?

Best,
Karen
___
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.


___
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] mris_make_face_parcellation

[Bruce Fischl]

Hi Karen

I guess I would do it in matlab - load the face parcellation and the 
aparc.annot, then count the number of vertices in each parcel in the face 
parcellation that is in a non-cortical aparc.annot parcel, and set a 
threshold for discarding them.


cheers
Bruce


On Wed, 2 Apr 2014, Karen Marie Sandø Ambrosen wrote:


Hi Bruce,

How can I remove the non-cortical parcels from the annotation file created
by mris_make_face_parcellation, such that I obtain an annotation file with
approx. the same number of parcels as ?h.aparc.annot.

Best,
Karen

On 04/01/2014 02:05 PM, Bruce Fischl wrote:
  Hi Karen

  sorry, I don't think so. You could certainly discard parcels
  that have a substantial non-cortical component to them, but
  parcellating the remainder of the surface uniformly isn't
  trivial.

  cheers
  Bruce
  On Tue, 1 Apr 2014, Karen Marie Sandø Ambrosen wrote:

Hi Freesurfer experts,

I first parcellated the ?h.aparc.annot using the
mris_divide_parcellation and at first glance it
seems fine. However, I
experienced that the size of the regions varies a
lot. I then found the
mris_make_face_parcellation, that parcellate the
surface in regions of
more equal sizes. Unfortunately the
mris_make_face_parcallation uses the
whole surface including the medial wall. Is there
any way I can get rid
of the labels covering the medial wall and obtain a
parcellation with
the same number of vertices as ?h.apac.annot, but
with regions of equal
size?

Best,
Karen
___
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-mai
l
contains patient information, please contact the Partners Compliance HelpLin
e at
http://www.partners.org/complianceline . If the e-mail was sent to you in er
ror
but does not contain patient information, please contact the sender and prop
erly
dispose of the e-mail.



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


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

Re: [Freesurfer] recon all with 7T data

[Xiaomin Yue]

Hi Joe,
Thanks for your response.  For the future reference, it also needs the 
parameter -notal-check, otherwise it will fail again.  Although the 
reconstruction was completed surprisingly without error, a significant amount 
of cortex in the top of the brain was cut off in the brain.mgz file.  It needs 
to be rerun after correcting that error(s).
Xiaomin 

> Date: Tue, 1 Apr 2014 19:52:53 -0400
> From: j...@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] recon all with 7T data
> 
> 
> hi Xiaomin,
> 
> 7T data can sometimes cause Talairach failures with the standard
> registration tools due to the strong bias fields. the Talairach
> transformation is used for identifying seed points, and the -use-mritotal
> flag just specifies that the MINC software will be used for the
> Talairach'ing.
> 
> see this page for more info:
>   http://freesurfer.net/fswiki/talairach?highlight=%28use%5C-mritotal%29
> 
> 
> -jon
> 
> 
> 
> 
> 
> 
> 
> On Fri, 28 Mar 2014, Xiaomin Yue wrote:
> 
> >
> > I tried to do surfer reconstruction (version 5.3) collected in SIEMENS
> > 7T, with error:  imgreg_4dfp
> > /opt/freesurfer-530/average/711-2C_as_mni_average_305
> > /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11
> > none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254.
> > This seems happened for many others.  However, the reconstruction worked
> > fine as using data collected from 3T, which means the freesurfer was
> > installed correct, and environment settings are correct as well.  Also,
> > the reconstruction on the 7T data can go through using additional
> > parameter: -use-mritotal.  My question is how the -use-mritotal
> > parameter would affect final surface?
> > Thanks for providing your input on this.
> > Xiaomin Yue
> >
> ___
> 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


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] quality T1 scans for new study

[Bruce Fischl]

Hi Jelmer

I took a quick look, but it is a lot easier for us if you extract the 
relevant parameters, as we are not that familiar with Philips in general. 
Is this inversion-prepared? I didn't see a TI. Generally 
inversion-preparation improves T1 CNR/unit-time. Also, your wrap direction 
looks like it is A/P.You might try making it L/R instead which is a shorter 
dimension. What coil are you using? Are you using sense?


cheers
Bruce


On Wed, 2 Apr 2014, Kok, JG (neuro) wrote:


Dear Bruce, Andre, someone else,

I think I caused some misunderstanding yesterday for which I am sorry. Now I do 
not know on what parameters Andre commented. So to hopefully make things clear 
I am once more attaching the parameter file which was used to create a T1 image 
(see attached screenshots) that may be of good quality. I hope you are willing 
to have a look and see if these parameters would result in good quaity T1 
images.

Thanks,

Jelmer



Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) 
[j.g.ko...@umcg.nl]
Verzonden: dinsdag 1 april 2014 18:17
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

Hi Andre,

I hope you looked at the attached "scan1_parameter_file.txt" when you mentioned that you 
think it seemed to be a reasonable protocol: the parameters in the body of the email Bruce is 
referring to were the suggested parameters in 
"http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf";, 
not the ones I am using/planning to adjust.

Thanks,

Jelmer



Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl 
[fis...@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 18:10
Aan: Freesurfer support list
CC: Andre van der Kouwe
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

no, I just looked at the ones in the body of your email
On Tue, 1 Apr 2014,
Kok, JG (neuro) wrote:


Dear Bruce and Andre,

PS I am sorry, but may I assume you have only looked at the parameters in 
"scan1_parameter_file.txt" and not in
"scan2_parameter_file.txt"? That would be fine, but I would just like to check 
we are talking about the same scan parameters
that seem to be fine...

Thanks,

Jelmer


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Kok, JG (neuro) 
[j.g.ko...@umcg.nl]
Verzonden: dinsdag 1 april 2014 16:45
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

Hi Bruce and Andre,

Many thanks for your comments!

Cheers,

Jelmer


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Andre van der Kouwe
[an...@nmr.mgh.harvard.edu]
Verzonden: dinsdag 1 april 2014 15:37
Aan: Bruce Fischl; Freesurfer support list
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

No, I think that's a reasonable protocol to use and good to use SENSE to speed 
it up.

 Original message 
From: Bruce Fischl
Date:04/01/2014 2:28 PM (GMT+02:00)
To: Freesurfer support list
Cc: Andre van der Kouwe
Subject: Re: [Freesurfer] quality T1 scans for new study

looks pretty reasonable. Andre: any comments/suggestions?

On Tue, 1 Apr
2014, Kok, JG (neuro) wrote:


Hi Bruce,

Thanks for your fast reply.

Hereby I attach the parameter files of both scans (although I suspect looking at the 
parameters of "scan1" may be sufficient).

Checking it with the information on Philips at
"http://www.nmr.mgh.harvard.edu/~andre/FreeSurfer_recommended_morphometry_protocols.pdf":


"
Sequence: T1W_3D_TFE_SENSE
Acquisition time: 5:13
Voxel size: 1.0 x 1.0 x 1.0 mm3
Geometry: FoV 256 mm (256 x 256 matrix), 176 sagittal slices, slice thickness 1 
mm, (3D encoding)
Timing: TR shortest (7600 ms), TI 1100 ms, TE shortest (3.5 ms), bandwidth 
191.5 Hz/px
RF: flip angle 7°
Acceleration: 2x SENSE
"

suggests that parameters in "scan1_parameter_file.txt" are already pretty 
similar to those I guess. (Is it the SENSE that is

missing in our protocol that is the most important difference?)


Thanks,

Jelmer


Van: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] namens Bruce Fischl

[fis...@nmr.mgh.harvard.edu]

Verzonden: dinsdag 1 april 2014 14:09
Aan: Freesurfer support list
Onderwerp: Re: [Freesurfer] quality T1 scans for new study

Hi Jelmer

if you give us the specific acquisition details we can help more (receive
coil, acceleration, voxel size, sequence type, TR/TE/TI/flip
angle/bandwidth, etc). We also have recommended morphometry sequences
on our 

Re: [Freesurfer] localgi make_outer_circle

[Marie Schaer]

Hi Charnjit,

I'm sorry I can't really help you on that, I'm not really familiar with matlab 
installation on a cluster. And given that lGI calls matlab repeatedly, if you 
want to split the process you may have to do it at several stages. But maybe 
someone else has an idea for the cluster and can jump in the discussion?

Sorry not to be of more help,

Marie

On Apr 2, 2014, at 1:58 PM, Charnjit Sidhu 
 wrote:

> Hi Maria,
> 
> The following are details of the problems we are having which I posted 
> earlier:
> 
> We have a user who is trying run a script that submits a recon-all job to our 
> cluster using the -localGI flag:
> 
> recon-all -subjid $i -localGI
> 
> I know this requires matlab which we have installed on the cluster however we 
> cannot submit matlab within a working node which the submitted node is trying 
> to do, we get the following error:
> 
> denied: host "hostname" is no submit host
> 
> I know what is causing the error, I just don't know how to fix it, as Matlab 
> cannot be run directly on this computer.
> 
> this message is given when the  make_outer_surface script matlab script is 
> submitted within the submitted job.
> 
> We have a script that allows matlab to run from within the cluster and have 
> tried to add this as an environment variable to the script:
> 
> matlab=matlab_cluster ; export matlab
> source $matlab
> 
> But when we add this it still fails with the same error,
> 
> Do you know how I can make changes to the script allowing us to run the above 
> script when matlab is called? Or are we missing something from our script? Or 
> should we split the process into a further script?
> 
> I have attached the relevant scripts and output.
> 
> Can you help me.
> 
> Thanks
> 
> Charnjit
> 
> 
> 
> 
> 
> 
> From: Marie Schaer [marie.sch...@unige.ch]
> Sent: 02 April 2014 12:45
> To: Freesurfer support list
> Cc: Charnjit Sidhu
> Subject: Re: [Freesurfer] localgi make_outer_circle
> 
> Hi Charnjit,
> 
> Can you copy / paste the error message? Otherwise I can't help you.
> 
> Best,
> 
> Marie
> 
> On Apr 2, 2014, at 12:54 PM, Charnjit Sidhu 
> wrote:
> 
>> Hi,
>> 
>> Does anyone know how matlab is called in the localgi process.
>> 
>> My script fails during the make_outer_circle process, I need to export some 
>> variables before Matlab is called to enable it to work on our cluster (i.e 
>> different matlab path, userid) . How can I change the way matlab is called?
>> 
>> Thanks
>> 
>> Charnjit
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> ___
>> 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
> 
> 
> 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] localgi make_outer_circle

[Charnjit Sidhu]

Hi Maria,
 
The following are details of the problems we are having which I posted earlier:

We have a user who is trying run a script that submits a recon-all job to our 
cluster using the -localGI flag:

recon-all -subjid $i -localGI

I know this requires matlab which we have installed on the cluster however we 
cannot submit matlab within a working node which the submitted node is trying 
to do, we get the following error:

denied: host "hostname" is no submit host

I know what is causing the error, I just don't know how to fix it, as Matlab 
cannot be run directly on this computer.

this message is given when the  make_outer_surface script matlab script is 
submitted within the submitted job.

We have a script that allows matlab to run from within the cluster and have 
tried to add this as an environment variable to the script:

matlab=matlab_cluster ; export matlab
source $matlab

But when we add this it still fails with the same error,

Do you know how I can make changes to the script allowing us to run the above 
script when matlab is called? Or are we missing something from our script? Or 
should we split the process into a further script?

I have attached the relevant scripts and output.

Can you help me.

Thanks

Charnjit






From: Marie Schaer [marie.sch...@unige.ch]
Sent: 02 April 2014 12:45
To: Freesurfer support list
Cc: Charnjit Sidhu
Subject: Re: [Freesurfer] localgi make_outer_circle

Hi Charnjit,

Can you copy / paste the error message? Otherwise I can't help you.

Best,

Marie

On Apr 2, 2014, at 12:54 PM, Charnjit Sidhu 
 wrote:

> Hi,
>
> Does anyone know how matlab is called in the localgi process.
>
> My script fails during the make_outer_circle process, I need to export some 
> variables before Matlab is called to enable it to work on our cluster (i.e 
> different matlab path, userid) . How can I change the way matlab is called?
>
> Thanks
>
> Charnjit
>
>
>
>
>
>
>
> ___
> 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_idbatch_LGI_50.sh
Description: freesurfer_idbatch_LGI_50.sh


recon12-emo04.sh
Description: recon12-emo04.sh


recon-all-emo04.o763358
Description: recon-all-emo04.o763358
___
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] localgi make_outer_circle

[Marie Schaer]

Hi Charnjit,

Can you copy / paste the error message? Otherwise I can't help you.

Best,

Marie

On Apr 2, 2014, at 12:54 PM, Charnjit Sidhu 
 wrote:

> Hi,
> 
> Does anyone know how matlab is called in the localgi process.
> 
> My script fails during the make_outer_circle process, I need to export some 
> variables before Matlab is called to enable it to work on our cluster (i.e 
> different matlab path, userid) . How can I change the way matlab is called?
> 
> Thanks
> 
> Charnjit
> 
> 
> 
> 
> 
> 
> 
> ___
> 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] localgi make_outer_circle

[Charnjit Sidhu]

Hi,

Does anyone know how matlab is called in the localgi process.

My script fails during the make_outer_circle process, I need to export some 
variables before Matlab is called to enable it to work on our cluster (i.e 
different matlab path, userid) . How can I change the way matlab is called?

Thanks

Charnjit







___
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] extracting mean thickness values across subjects from qdec clusters

[Tudor Popescu]

>
>> Your mri_glmfit-sim command line is not correct and does not match
>> examples in the help. Basically you need to spec "--cache 1.3 abs"
>> not "--cache 1.3 --sim-sign abs"
>>
>> Thanks Doug, now it worked, however I'm getting this error, which several
>> other people seem to get: "Computing spatial average of each frame
>>   0  1  2*** glibc detected *** mri_segstats: malloc(): memory
>> corruption: 0x2e8df328 ***". I am running FS 5.3.0 through VirtualBox, 2GB
>> ram allocated.
>>
> What is your full command line? Sometimes this happens when setting the
> cwp to 1 (or close to 1).
>

My command was
 mri_glmfit-sim --glmdir
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh --cache 1.3 abs
therefore I did not change the --cwpvalthresh input argument, meaning cwp
presumably stayed at its default of .05.
Terminal output is attached.
What else can I try to make this command work?
fsuser@xubuntu-VirtualBox:~$ mri_glmfit-sim --glmdir 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh --cache 1.3 abs
cmdline mri_glmfit --y 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/y.mgh --fsgd 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/qdec.fsgd dods --glmdir 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh --surf fsaverage lh --label 
/media/math/all38subj/fsaverage/label/lh.aparc.label --C 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/contrasts/lh-Avg-Intercept-pial_lgi.mat
 --C 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/contrasts/lh-Avg-pial_lgi-DFAbhv-Cor.mat
 --C 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/contrasts/lh-Diff-F-M-Intercept-pial_lgi.mat
 --C 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/contrasts/lh-Diff-F-M-Cor-pial_lgi-DFAbhv.mat
SURFACE: fsaverage lh
log file is 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/cache.mri_glmfit-sim.log

cd /home/fsuser
/usr/local/freesurfer/bin/mri_glmfit-sim
--glmdir /media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh --cache 1.3 abs

$Id: mri_glmfit-sim,v 1.36.2.5 2012/10/01 22:31:37 greve Exp $
Wed Apr  2 00:10:54 BST 2014
Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 
UTC 2012 i686 i686 i386 GNU/Linux
fsuser
setenv SUBJECTS_DIR /media/math/all38subj
FREESURFER_HOME /usr/local/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/y.mgh --fsgd 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/qdec.fsgd dods --glmdir 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh --surf fsaverage lh --label 
/media/math/all38subj/fsaverage/label/lh.aparc.label --C 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/contrasts/lh-Avg-Intercept-pial_lgi.mat
 --C 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/contrasts/lh-Avg-pial_lgi-DFAbhv-Cor.mat
 --C 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/contrasts/lh-Diff-F-M-Intercept-pial_lgi.mat
 --C 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/contrasts/lh-Diff-F-M-Cor-pial_lgi-DFAbhv.mat

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 22.238537
CSD 
/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm22/abs/th13/mc-z.csd
mri_surfcluster --in 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/lh-Avg-Intercept-pial_lgi/sig.mgh
 --csd 
/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm22/abs/th13/mc-z.csd
 --mask /media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/mask.mgh --cwsig 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/lh-Avg-Intercept-pial_lgi/cache.th13.abs.sig.cluster.mgh
 --vwsig 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/lh-Avg-Intercept-pial_lgi/cache.th13.abs.sig.voxel.mgh
 --sum 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/lh-Avg-Intercept-pial_lgi/cache.th13.abs.sig.cluster.summary
 --ocn 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/lh-Avg-Intercept-pial_lgi/cache.th13.abs.sig.ocn.mgh
 --oannot 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/lh-Avg-Intercept-pial_lgi/cache.th13.abs.sig.ocn.annot
 --annot aparc --csdpdf 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/lh-Avg-Intercept-pial_lgi/cache.th13.abs.pdf.dat
 --cwpvalthresh .05 --o 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/lh-Avg-Intercept-pial_lgi/cache.th13.abs.sig.masked.mgh
 --no-fixmni --surf white
Creating CDFs from CSD files
csd->threshsign = 0
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
hemi   = lh
srcid  = 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/lh-Avg-Intercept-pial_lgi/sig.mgh
 
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = abs
thmin  = 1.3
thmax  = -1
fdr= -1
minarea= 0
xfmfile= talairach.xfm
nth = -1
outid= 
/media/math/all38subj/qdec/A2SepGroup_C_DODS_lgi_lh/lh-Avg-Intercept-pial_lgi/cache.th13.abs.sig.masked.mgh
 MGH
ocnid= 
/me

Re: [Freesurfer] Cortical thickness measurement using Freesurfer v 5.3

[Saurabh Thakur]

Hello Everyone,

I got the answer in mri_annotation2label.

I new to freesurfer and trying to learn as fast as possible.

Thanks for patience and cooperation.

cheers
Saurabh Thakur,






On Wed, Apr 2, 2014 at 10:58 AM, Saurabh Thakur  wrote:

> Hello Freesurfer Expert,
>
> I am trying for measurement of cortical thickness using Freesurfer v5.3.
> I have getting values for cortical thickness, surface area and gray matter
> volume using stats/rh.aparc.a2009.stats file.
> But i am looking for general value for entire Frontal,Temporal, parietal
> and occipital lobe, and not very specific region wise value. Is is possible
> to get avg thickness value for all lobes? and If possible how to get that..?
>
> Thanks in advanced,
> Saurabh Thakur,
>
>
>
>
>
>
___
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] preprocessing question

[Eiran Harel]

Thanks Doug, i downloaded it and now the file exists:

$FREESURFER_HOME/bin/fslmaths.fsl

Unfortuantely it is still not running and gives the same error when running 
preproc-sess:

mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1 -ndil 1 
-nerode 0
ERROR: cannot find either fslmaths for avwmaths

How can i proceed?
Thanks,
Eiran

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, April 02, 2014 12:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] preprocessing question

thanks, it must be something in our distribution script affecting mac

On 04/01/2014 05:13 PM, Markus Gschwind wrote:
> Thanks Doug,
>
> I notice that on my Mac
> build freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
>
> ...I don't have fslmaths.fsl neither. There are only
>
> $ which $FREESURFER_HOME/bin/fsl*
> /Applications/freesurfer/bin/fsl_label2voxel
> /Applications/freesurfer/bin/fsl_rigid_register
> /Applications/freesurfer/bin/fsl_sub_mgh
> /Applications/freesurfer/bin/fslregister
>
> $ which $FREESURFER_HOME/bin/*.fsl
> /Applications/freesurfer/bin/epidewarp.fsl
> /Applications/freesurfer/bin/fscalc.fsl
> /Applications/freesurfer/bin/mri_motion_correct.fsl
>
> (I never executed the above mentioned process of Eiran thoug...)
>
> Best,
> Markus
>
>
>
>
>
> 2014-04-01 18:36 GMT+02:00 Douglas N Greve  >:
>
> That is weird. You can get a copy from here
>
> 
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslmaths.fsl.mac
>
> copy it to
>
> $FREESURFER_HOME/bin/fslmaths.fsl
>
>
> On 04/01/2014 12:25 PM, Eiran Harel wrote:
> > Hi Doug,
> > No, it does not exist.
> > What should i do?
> > Thanks,
> > Eiran
> > 
> > From: freesurfer-boun...@nmr.mgh.harvard.edu
> 
> [freesurfer-boun...@nmr.mgh.harvard.edu
> ] on behalf of
> Douglas N Greve [gr...@nmr.mgh.harvard.edu
> ]
> > Sent: Tuesday, April 01, 2014 7:16 PM
> > To: freesurfer@nmr.mgh.harvard.edu
> 
> > Subject: Re: [Freesurfer] preprocessing question
> >
> > does $FREESURFER_HOME/bin/fslmaths.fsl exist?
> >
> > On 04/01/2014 03:59 AM, Eiran Harel wrote:
> >> Dear freesurfers,
> >> I have installed freesurfer and fsl on my Mac:
> >> *
> >> *
> >> * freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> *
> >> *Setting up environment for FreeSurfer/FS-FAST (and FSL)*
> >> *FREESURFER_HOME   /Applications/freesurfer*
> >> *FSFAST_HOME /Applications/freesurfer/fsfast*
> >> *FSF_OUTPUT_FORMAT nii.gz*
> >> *SUBJECTS_DIR  /Applications/freesurfer/subjects*
> >> *MNI_DIR /Applications/freesurfer/mni*
> >> *FSL_DIR   /usr/local/fsl*
> >>
> >> I am trying to run Preproc-sess command:
> >>
> >> *preproc-sess -s bsmt102 -surface fsaverage lhrh -mni305 -fwhm
> 5 -fsd
> >> bold -stc odd -per-run -force*
> >>
> >> and get this error:
> >>
> >> *mkbrainmask -i template.nii.gz -o masks/brain.nii.gz -thresh 0.1
> >> -ndil 1 -nerode 0*
> >> *ERROR: cannot find either fslmaths for avwmaths*
> >> *
> >> *
> >> Any suggestions?
> >> Thanks!
> >> Eiran
> >>
> >>
> >>
> >>
> >> 
> >> 
> >>    
> >> 
> >>
> >>
> >>
> >>
> >> ___
> >> 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://m