Re: [Freesurfer] make_average_subject command error

elsewhere.) Many thanks! Best, Asuka From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: 07 February 2024 14:33 To: Freesurfer support list Subject: Re: [Freesurfer] make_average_subject command error If you run recon-all, ?h.pial

Re: [Freesurfer] make_average_subject command error

e each link, for example, 'ln -s lh.pial.T1 lh.pial' Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Asuka Toyofuku Sent: Wednesday, February 7, 2024 5:13 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] make_average_subject command error

[Freesurfer] make_average_subject command error

External Email - Use Caution Dear Freesurfer experts, We're trying to make an average subject for group analysis using Freesurfer 7.1, but the make_average_subject command exits with errors after calling make_average_surf: MakeAverageSurf(): 129 lh pial sphere.reg talairach.x

Re: [Freesurfer] make_average_subject without Talairach transform

Associate McGill University MD Anderson Cancer Centre -- From: on behalf of Trisanna Sprung-Much Reply-To: Freesurfer support list Date: Wednesday, April 14, 2021 at 7:32 PM To: Freesurfer support list Subject: Re: [Freesurfer] make_average_subject without Talairach transform External Email

Re: [Freesurfer] make_average_subject error

When I look at the README, this is the contents. Are you looking at https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/README ? Download make_average_subject and the platform-specific version of mri_aparc2aseg from this directory and move them to your freesurfer bin directory v

Re: [Freesurfer] make_average_subject without Talairach transform

quot;freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] make_average_subject without Talairach transform If you have the transform in the form of an LTA file, I think all you need to do is put it in the subject/mri/transforms folder, then spec --xfrom your.lta when running make_ave

Re: [Freesurfer] make_average_subject error

External Email - Use Caution The patch (see text below) only directed me to replace a file in the freesurfer/gcc/lib directory, which I did. Do I also need to replace the make_average_subject and mri_aparc2aseg files in my freesurfer bin? *To patch the existing 6.0.0 release you m

Re: [Freesurfer] make_average_subject error

It looks like you are still using the old make_average_subject as the time stamp is from Jan 19, 2017 (same for mri_aparc2aseg). Can you confirm that those are really the patches? On 3/29/2021 12:52 PM, Jordan Mullins wrote: External Email - Use Caution Hi Douglas, Just following up

Re: [Freesurfer] make_average_subject error

External Email - Use Caution Hi Douglas, Just following up on this. Thanks! On Wed, Mar 17, 2021 at 6:12 PM Jordan Mullins wrote: > Yes! Results attached. > > On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve > wrote: > >> >> Can you run >> ls -l $FREESURFER_HOME/bin/mri_aparc2

Re: [Freesurfer] make_average_subject without Talairach transform

2021 at 11:36 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] make_average_subject without Talairach transform If you have the transform in the form of an LTA file, I think all you need to do is put it in the subject/mri/transforms folder, then spec --xfrom yo

Re: [Freesurfer] make_average_subject without Talairach transform

average chimp volume”. Trisanna -- *From: * on behalf of "Douglas N. Greve" *Reply-To: *Freesurfer support list *Date: *Thursday, March 25, 2021 at 11:24 AM *To: *"freesurfer@nmr.mgh.harvard.edu" *Subject: *Re: [Freesurfer] make_average_subject without Talairach tran

Re: [Freesurfer] make_average_subject without Talairach transform

“in the space of the average chimp volume”. Trisanna -- From: on behalf of "Douglas N. Greve" Reply-To: Freesurfer support list Date: Thursday, March 25, 2021 at 11:24 AM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] make_average_subject without Talaira

Re: [Freesurfer] make_average_subject without Talairach transform

Associate McGill University MD Anderson Cancer Centre -- *From: * on behalf of "Fischl, Bruce" *Reply-To: *Freesurfer support list *Date: *Thursday, March 25, 2021 at 10:59 AM *To: *Freesurfer support list *Subject: *Re: [Freesurfer] make_average_subject without Talairach transform

Re: [Freesurfer] make_average_subject without Talairach transform

If you don't have a transform, how will you align the subjects into a common space? On 3/25/2021 10:19 AM, Trisanna Sprung-Much wrote: External Email - Use Caution External Email - Use Caution Hi there I’d like to know if it is possible to create an average volume and avera

Re: [Freesurfer] make_average_subject without Talairach transform

ruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Trisanna Sprung-Much Sent: Thursday, March 25, 2021 10:19 AM To: Freesurfer support list Subject: [Freesurfer] make_average_subject without Talairach transform External Email - Use Caution External Email - Use Cautio

Re: [Freesurfer] make_average_subject without Talairach transform

...@nmr.mgh.harvard.edu On Behalf Of Trisanna Sprung-Much Sent: Thursday, March 25, 2021 10:19 AM To: Freesurfer support list Subject: [Freesurfer] make_average_subject without Talairach transform External Email - Use Caution External Email - Use Caution Hi there I’d like to know if it is

[Freesurfer] make_average_subject without Talairach transform

External Email - Use Caution Hi there I’d like to know if it is possible to create an average volume and average surface of several subjects without having to incorporate the Talairach transform and no transform at all. Thank you, Trisanna Sprung-Much Research Associate McGill

Re: [Freesurfer] make_average_subject error

External Email - Use Caution Yes! Results attached. On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve wrote: > > Can you run > ls -l $FREESURFER_HOME/bin/mri_aparc2aseg > $FREESURFER_HOME/bin/make_average_subject > and send the result? > > Also, the result of > which mri_aparc2as

Re: [Freesurfer] make_average_subject error

Can you run ls -l $FREESURFER_HOME/bin/mri_aparc2aseg $FREESURFER_HOME/bin/make_average_subject and send the result? Also, the result of which mri_aparc2aseg which make_average_subject On 3/17/2021 8:36 PM, Jordan Mullins wrote: External Email - Use Caution Yes, I had seen that r

Re: [Freesurfer] make_average_subject error

External Email - Use Caution Yes, I had seen that report and had downloaded the patch, but still got the same error. Are there any other steps I can take? On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve wrote: > This problem is documented (along with a fix) on our release notes

Re: [Freesurfer] make_average_subject error

This problem is documented (along with a fix) on our release notes https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes On 3/16/2021 3:39 PM, Jordan Mullins wrote: External Email - Use Caution Yes, I used the make_average_subject command. I've attached a text file below of the comm

Re: [Freesurfer] make_average_subject error

What command are you using? make_average_subject? Send the command line and terminal output On 3/10/2021 3:53 PM, Jordan Mullins wrote: External Email - Use Caution Hello, I am trying to create an average subject from a set of subjects, but keep getting an error that says "mghRead(m

[Freesurfer] make_average_subject error

External Email - Use Caution Hello, I am trying to create an average subject from a set of subjects, but keep getting an error that says "mghRead(mri/norm.mgz, -1): could not open file". I've read that several others have solved this issue by installing the patch available at http

Re: [Freesurfer] make_average_subject

dev or 7beta On 2/29/2020 10:24 AM, Benjamin Ineichen wrote: External Email - Use Caution Ok. It says that for mac, I need to download the dev release, I assume that refers to Freesurfer version 7.0? Am Fr., 28. Feb. 2020 um 22:15 Uhr schrieb Douglas N. Greve mailto:dgr...@mgh.harv

Re: [Freesurfer] make_average_subject

External Email - Use Caution Respected want to do a Structural based analysis which constitutes of volume and area, can i correlate or make relation of tracks with same subject. regards On Sat, 29 Feb 2020, 20:56 Benjamin Ineichen, wrote: > External Email - Use Cautio

Re: [Freesurfer] make_average_subject

External Email - Use Caution Ok. It says that for mac, I need to download the dev release, I assume that refers to Freesurfer version 7.0? Am Fr., 28. Feb. 2020 um 22:15 Uhr schrieb Douglas N. Greve < dgr...@mgh.harvard.edu>: > Look at the release notes for how to resolve this >

Re: [Freesurfer] make_average_subject

Look at the release notes for how to resolve this http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes On 2/26/2020 4:34 AM, Benjamin Ineichen wrote: External Email - Use Caution Dear Freesurfer experts, I want to create a new standard template from my study population. For this, I

Re: [Freesurfer] make_average_subject

External Email - Use Caution As addendum to my message. The full terminal output: Reading surface /Users/benine/Desktop/PVS_validation_cohort/MyelinMS_MRI_export/Freesurfer_output/REMY001_M0//surf/lh.white Loading annotations from /Users/benine/Desktop/PVS_validation_cohort/My

[Freesurfer] make_average_subject

External Email - Use Caution Dear Freesurfer experts, I want to create a new standard template from my study population. For this, I thought about using make_average_subject. Thus, I run: make_average_subject --out avgsubject --subjects REMY001 REMY002 REMY003 I get an error mess

Re: [Freesurfer] make_average_subject error

lf of Maxime Perron <maxime.perro...@ulaval.ca> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu> Date: Friday, September 6, 2019 at 5:08 PM To: FS Help <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] make_average_subject error   External Email - Us

Re: [Freesurfer] make_average_subject error

at 5:08 PM To: FS Help Subject: Re: [Freesurfer] make_average_subject error External Email - Use Caution ​Hi Douglas, I'm sorry for the misunderstanding! Thanks for the command. I attached the mas.log. Cheers, Maxime ​ De : freesurfer

Re: [Freesurfer] make_average_subject error

surfer_S156" "Freesurfer_S158" "Freesurfer_S164" --out BrainaverageN72 cd /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM/Analyse_morpho/Subject_data/BrainaverageN72 mkdir ori cd /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_I

Re: [Freesurfer] make_average_subject error

"Freesurfer_S151" "Freesurfer_S152" >> "Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" >> "Freesurfer_S158" "Freesurfer_S164" --out BrainaverageN72 >> >> cd >> /V

Re: [Freesurfer] make_average_subject error

quot; > "Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" > "Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" > "Freesurfer_S153" "Freesurfer_S

Re: [Freesurfer] make_average_subject error

ot; "Freesurfer_S152" "Freesurfer_S153" "Freesurfer_S154" "Freesurfer_S155" "Freesurfer_S156" "Freesurfer_S158" "Freesurfer_S164" --out BrainaverageN72 cd /Volumes/Groups/tremblay/Projets/Projet_192_2017_Chant_PascaleT/Etude2_IRM

Re: [Freesurfer] make_average_subject error

Is BrainaverageN72 in the subjects list? On 9/3/19 12:39 PM, Maxime Perron wrote: > > External Email - Use Caution > > ​Dear Freesurfer Experts, > > > I have the following issue when running the make_average_subject command ( > > make_average_subject --subjects (Subjid) --out BrainaverageN

[Freesurfer] make_average_subject error

External Email - Use Caution ​Dear Freesurfer Experts, I have the following issue when running the make_average_subject command ( make_average_subject --subjects (Subjid) --out BrainaverageN72) :  Building hash of lh white Building hash of lh pial Building hash of r

[Freesurfer] make_average_subject error

External Email - Use Caution Dear all, I have seen this error mentioned several times on the list but I have never seen a solution posted. It is claimed that there is a patch and a README that explains the patch at: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-pat

Re: [Freesurfer] make_average_subject error: could not load norm volume from (null)

I think it is crashing outside of make_average_surface and make_average_volume, so the log files are not telling me what is going on. Can you capture the full terminal output? Also, you can try it with two subjects so that it runs faster (but it might not crash). On 7/10/2019 5:39 AM, Mads Jen

Re: [Freesurfer] make_average_subject error: could not load norm volume from (null)

Can you send the full terminal output of make_average_subject? There should also be some log files (make_average_volume.log and make_average_surface.log) in the average subject that would be helpful On 7/4/2019 4:36 AM, Mads Jensen wrote: External Email - Use Caution HI FreeSurfer Deve

[Freesurfer] make_average_subject error: could not load norm volume from (null)

External Email - Use Caution HI FreeSurfer Developers, I'm attempting to create an average subject make_average_subject but I get the error message the following error when I run the make_average_command: Loading aseg from REMOVED-PATH/avg_elder/mri/aseg.presurf.hypos.mgz ASeg Vo

Re: [Freesurfer] make_average_subject error

External Email - Use Caution Hi Douglas, Yes - attached here is the make_average_subject.log file. The command used was: make_average_subject --out average_v2 --subjects $(cat subjects.txt) subjects.txt also attached. Thanks again for your help Colleen setenv SUBJECTS_DIR /lustr

Re: [Freesurfer] make_average_subject error

Can you send the make_average-subject command and log file? On 9/21/18 7:03 AM, C.P.E. Rollins wrote: External Email - Use Caution Hello Freesurfer Developpers, I'm attempting to make a study specific template using all of my subjects as input using the make_average_subject command, but a

[Freesurfer] make_average_subject error

External Email - Use Caution Hello Freesurfer Developpers, I'm attempting to make a study specific template using all of my subjects as input using the make_average_subject command, but am receiving the following error: Building hash of lh white Building hash of lh pial Build

Re: [Freesurfer] make_average_subject error

Hi Xiaoyu how are you trying to create an average subject? It looks like you are running recon-all on something. Typically we use the script make_average_subject for this cheers Bruce On Wed, 11 Jul 2018, Wang, Xiaoyu wrote: External Email - Use Caution   Hello FreeSurf

[Freesurfer] make_average_subject error

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to perform group analysis on a group of subjects. However, When I am trying to create an average subject I get the following error. mghRead(mri/norm.mgz, -1) could not open file I went into the average fo

Re: [Freesurfer] make_average_subject monkey data

That worked! Thanks a lot :) I suppose that I could improve the appearance with some further manual editing of the surfaces. Best Francesca 2018-03-16 16:17 GMT+01:00 Douglas Greve : > Try this: > > 1. make a back up of the talairach.xfm > > cp talairach.xfm bak.talarach.xfm > > 2. Convert the l

Re: [Freesurfer] make_average_subject monkey data

Thanks Doug! Actually talairach.lta looks quite good. However, when I tried to make_average_subject with --xform talairach.lta I got immediately an error: make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkey --xform talairach.lta setenv SUBJECTS_DIR /usr/local/freesurfer/subj

Re: [Freesurfer] make_average_subject monkey data

See if the talairach.lta is any better, eg cd subject/mri/transforms tkregister --mov ../nu.mgz --s fsaverage --reg talairach.lta If so, you can try running make_average_subject with --xform talairach.lta I've never done this, but it might work :) On 03/15/2018 01:02 PM, Francesca Strappini

Re: [Freesurfer] make_average_subject monkey data

Thank you, Doug! One monkey has a pretty decent registration while the other one does not even appear in the window when I try to manually check the registration with this command line: tkregister --mgz --s MonkeyCelia --fstal --surf orig It looks like if there is no brain. 2018-03-15 16:57 GMT+01

Re: [Freesurfer] make_average_subject monkey data

Check the talairach.xfm registration. It is probably way off. It does not have to be perfect (esp since they are different species), but the two subjects should have a similar registration On 03/14/2018 07:27 PM, Francesca Strappini wrote: > Both average hemispheres look very bad, they don't ev

Re: [Freesurfer] make_average_subject monkey data

Both average hemispheres look very bad, they don't even look like a brain. The two monkey surfaces look reasonable, except for some topological defect that I think could be fixed with some manual editing. Is there anything I could try? Thanks a lot Francesca 2018-03-14 23:41 GMT+01:00 Douglas N.

Re: [Freesurfer] make_average_subject monkey data

I don't know what is going on there except that the average surfaces are probably wrong in some way. It looks like it made it all the way through except for that step, so all of the output should be there. How does it look? On 03/13/2018 05:27 PM, Francesca Strappini wrote: > Dear Experts, > >

[Freesurfer] make_average_subject monkey data

Dear Experts, I'm trying to average two monkey brains. I run this command line: make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkeys but it ended with errors. I run the recon-all for both monkyes with the option -notal-check because I had problems with the Talairach regist

Re: [Freesurfer] make_average_subject label files

What do you mean you only get one vertex for the medial wall? Can you send the make_average_{subject,surface,volume}.log files (located in the scripts folder of the average subject) On 11/22/2017 05:01 AM, M del Mar Velasco wrote: > > Dear Freesurfer experts, > > > I have a question related to

[Freesurfer] make_average_subject label files

Dear Freesurfer experts, I have a question related to make_average_subject command and Freesurfer versions. When I used to create my average subject with Freesurfer 5.3, I got lh.cortex.label and rh.cortex.label files inside label folder with 149955 vertexs. Moreover, lh.Medial_Wall.label and

Re: [Freesurfer] make_average_subject error

Please see the attached log file. Thanks, Tugce On 11/16/17, 11:35 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve" wrote: can you send the entire log file? On 11/16/2017 11:32 AM, Duran, Tugce wrote: > > Dear FreeSurfer Experts, > >

Re: [Freesurfer] make_average_subject error

can you send the entire log file? On 11/16/2017 11:32 AM, Duran, Tugce wrote: > > Dear FreeSurfer Experts, > > I’m recently getting an error in make_average_subject and can’t find > the reason. > > Please see the following for the error log from recon-all.log: > > *Loading aseg from > /gpfs/pro

[Freesurfer] make_average_subject error

Dear FreeSurfer Experts, I’m recently getting an error in make_average_subject and can’t find the reason. Please see the following for the error log from recon-all.log: Loading aseg from /gpfs/projects/RadImagSci/CFN/test-SDA-import/VTRAK4/xserveraids/vtrak4/mci/IMAGENE/NIFTI_CENTRAL/IMAGENE_BL_

[Freesurfer] Make_average_subject

Dear Freesurfer Experts, I received this error while running the make_avg_subject script. I would greatly appreciate it if you can point me in the right direction. Also, I do not know how the aparc.annot file is supposed to be created. not aligning hemispheres before averaging. zeroing medial w

Re: [Freesurfer] make_average_subject for subcortical volumes in children

Hi Kristi yes, that is correct. Everything is stored in native space and all processing is done there until you start doing group-level stuff cheers Bruce On Fri, 17 Jul 2015, Kristi Griffiths wrote: Dear FS experts,   I am new to freesurfer and have a few basic questions.   I have

[Freesurfer] make_average_subject for subcortical volumes in children

Dear FS experts, I am new to freesurfer and have a few basic questions. I have a sample of 8-17 year olds in which I will be looking at both cortical thickness and subcortical volumes. I understand that the surface-based registrations seem to be fine for this age range (as per Ghosh et al, 201

Re: [Freesurfer] make_average_subject

> On 6 May 2015, at 16:49, Douglas N Greve wrote: > > memory should not be a problem > > On 05/06/2015 08:33 AM, Bruce Fischl wrote: >> Hi Jane >> >> we don't really see much blurring of folding patterns with the >> high-dimensional spherical warp so you might as well use them all >> (although

Re: [Freesurfer] make_average_subject

memory should not be a problem On 05/06/2015 08:33 AM, Bruce Fischl wrote: > Hi Jane > > we don't really see much blurring of folding patterns with the > high-dimensional spherical warp so you might as well use them all > (although there might be issues with memory - perhaps Doug can comment if >

Re: [Freesurfer] make_average_subject

no, sorry. I'll leave that for Doug and Marie Bruce On Wed, 6 May 2015, Jane Garrison wrote: Thanks so much Bruce. I also posted yesterday asking about whether it was possible to get LGI values for a spherical ROI based on a particular mni coordinate (I’ve been using Qdec so far for group a

Re: [Freesurfer] make_average_subject

Thanks so much Bruce. I also posted yesterday asking about whether it was possible to get LGI values for a spherical ROI based on a particular mni coordinate (I’ve been using Qdec so far for group analysis but can’t work out how to draw the ROI nor how to pull the LGI values. Would you have an

Re: [Freesurfer] make_average_subject

Hi Jane we don't really see much blurring of folding patterns with the high-dimensional spherical warp so you might as well use them all (although there might be issues with memory - perhaps Doug can comment if this is still true). cheers Bruce On Wed, 6 May 2015, Jane Garrison wrote: > >

[Freesurfer] make_average_subject

Hi, I have a question about the utility of the make_average_subject command. I have a schizophrenia study with 115 subjects and am worried about using the Freesurfer average brain, given that scz patients have distinct morphological aspects to their brains. I am therefore considering making

Re: [Freesurfer] Make_average_subject

No, the individual subjects processed by recon-all -all are all OK (not cut off superiorly), only the average produced by make_average_subject is cut off superiorly. Thanks Cheers Jürgen On [DATE], "Bruce Fischl" <[ADDRESS]> wrote: > Does it happen with just one subject? If so, can you upload i

Re: [Freesurfer] Make_average_subject

Does it happen with just one subject? If so, can you upload it? Thanks Bruce > On Oct 22, 2013, at 5:21 AM, Jürgen Hänggi > wrote: > > Hi Bruce > > I am running FS 5.3.0 on Mac OSX and both versions > > Lion OX X 10.7 (64b Intel) and > SnowLeopard OS X 10.6 (32b Intel) > > are affected. Howe

Re: [Freesurfer] Make_average_subject

Hi Bruce I am running FS 5.3.0 on Mac OSX and both versions Lion OX X 10.7 (64b Intel) and SnowLeopard OS X 10.6 (32b Intel) are affected. However, the average surface model looks fine. Cheers Jürgen On [DATE], "Bruce Fischl" <[ADDRESS]> wrote: > what version are you running? > On Tue, 22 Oct

Re: [Freesurfer] Make_average_subject

what version are you running? On Tue, 22 Oct 2013, J?rgen H?nggi wrote: > Dear FS experts > > When using make_average_subject the resulting volume files (T1.mgz, > orig.mgz, brain.mgz, etc.) are cut off superiorly (see attachment). > > Any idea? > > Thanks in advance > Regards > J?rgen > > ---

Re: [Freesurfer] make_average_subject without aparc and talairach.xfm

Hi Doug, just a quick follow-up on my previous questions regarding custom average surfaces. I guess I am a bit confused regarding the relationship of custom templates and custom average surfaces. I made a custom template and a custom average surface. However, I don't understand how they are related

Re: [Freesurfer] make_average_subject without aparc and talairach.xfm

You can just copy in the T1.mgz from fsaverage (won't matter that it is human), or you can try running make_average_volume to make a NHP volume. Not sure that will work, but make sure to use --no-aseg doug On 8/19/13 8:43 PM, Caspar M. Schwiedrzik wrote: Hi Doug, I ran make_average_surfac

Re: [Freesurfer] make_average_subject without aparc and talairach.xfm

Hi Doug, I ran make_average_surface.no-aparc and identity matrices on my data, and I seems to have completed the averaging without an error. However, when I try to view the result with tksurfer, I get an error because there is no average T1 for the average subject. How would you recommend I go abou

Re: [Freesurfer] make_average_subject without aparc and talairach.xfm

I would probably just try to do it by hand. Copy a file with the identity matrix into the right folder, then run tkregister2 --fstal --s subject It will bring the human atlas up. I would then play with it a little bit to get it to look ok. For surface-based applications, it will have no effec

Re: [Freesurfer] make_average_subject without aparc and talairach.xfm

Hi Doug, that's great, thank you very much. >From the previous posts I assume that this does not solve the issue with the missing Talairach.xfm. Do you have a recommendation for that? Thanks, Caspar 2013/8/19 Douglas N Greve > > I've put that script here > > > ftp://surfer.nmr.mgh.harvard.edu/t

Re: [Freesurfer] make_average_subject without aparc and talairach.xfm

I've put that script here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc On 08/19/2013 02:53 PM, Caspar M. Schwiedrzik wrote: > Hi Freesurfer experts, > I am trying to make an average surface from several monkey surfaces, > and I ran into a problem

[Freesurfer] make_average_subject without aparc and talairach.xfm

Hi Freesurfer experts, I am trying to make an average surface from several monkey surfaces, and I ran into a problem with make_average_subject. Specifically, I do not have an aparc file nor a talairach.xfm. It seems that these problems have come up on the list before ( http://www.mail-archive.com/f

Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

Thank you, doug, I will try xfm! On Thu, Mar 7, 2013 at 7:03 PM, Douglas N Greve wrote: > The xform has to be linear in the xfm format. The m3z cannot be used. > doug > > On 03/07/2013 06:44 PM, Xiaowei Song wrote: > > Thanks for your help. > > > > My command line is > > make_average_subject --o

Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

The xform has to be linear in the xfm format. The m3z cannot be used. doug On 03/07/2013 06:44 PM, Xiaowei Song wrote: > Thanks for your help. > > My command line is > make_average_subject --out avgGrp139 --subjects `cat > script/subjects.id ` --xform talairach.m3z > > > On Th

Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

Thanks for your help. My command line is make_average_subject --out avgGrp139 --subjects `cat script/subjects.id` --xform talairach.m3z On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl wrote: > what was your command line? > > On Thu, 7 Mar 2013, Xiaowei Song wrote: > > Sorry, I did not make it c

Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

what was your command line? On Thu, 7 Mar 2013, Xiaowei Song wrote: Sorry, I did not make it clear. In make_average_volume.log, the error message is: 1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013 mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni30

Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

Sorry, I did not make it clear. In make_average_volume.log, the error message is: 1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013 mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z -

Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

sorry, I don't understand. What was the error? I don't see one in this email. Can you send us the actual screen output? cheers Bruce On Thu, 7 Mar 2013, Xiaowei Song wrote: This error may come from regio_read_mincxfm function in registerio.c.Does this mean something wrong in recon-all? I forg

Re: [Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

This error may come from regio_read_mincxfm function in registerio.c. Does this mean something wrong in recon-all? I forgot to mention that FreeSurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song wrote: > Hi all, > > Did you encount

[Freesurfer] make_average_subject error: talairach.m3z does not start as 'MNI Transform File'

Hi all, Did you encounter the error message talairach.m3z does not start as 'MNI Transform File' when making average of subjects? I checked all the recon-all.log file and did not find error, but when running make_average_subject after recon-all, then this error shoot. To repeat the error message

[Freesurfer] make_average_subject error

Hello, I am trying to run Surface Group Analysis with Qdec, but am stuck on the "make_average_subject" step. I have run this command on four subjects in my virtual machine and everything is fine. However, I have 13 subjects and there is not enough room in the virtual machine for them. I have m

Re: [Freesurfer] make_average_subject

It might be failing on the aseg, so try it with --no-aseg doug Bruce Fischl wrote: > Hi Sonya > > did you run out of RAM? How much is on your machine? > > cheers > Bruce > > On Fri, 23 Mar 2012, sonya kaur wrote: > > >> Dear all,I'm getting an error with the make_average_subject command on >> f

Re: [Freesurfer] make_average_subject

Hi Sonya did you run out of RAM? How much is on your machine? cheers Bruce On Fri, 23 Mar 2012, sonya kaur wrote: > Dear all,I'm getting an error with the make_average_subject command on > freesurfer. The error is vm_allocate (size=262144) failed (error code 3). > According to the freesurfer he

[Freesurfer] make_average_subject

Dear all, I'm getting an error with the make_average_subject command on freesurfer. The error is vm_allocate (size=262144) failed (error code 3). According to the freesurfer helpdesk, it seems to be a problem with creating an "average" aseg. Is there any solution for this that you know of? Thank y

Re: [Freesurfer] make_average_subject failure

did you run out of disk space? Does that path exist? On Thu, 22 Mar 2012, Klein, Holger wrote: Dear Freesurfers,  Command line: make_average_subject --out average --subjects ... (n=60)  . . . . . Applying LTAtransformInterp (resample_type 1) writing to/Volumes/Macintosh/freesurfer/Kontrollen/

[Freesurfer] make_average_subject failure

Dear Freesurfers, Command line: make_average_subject --out average --subjects ... (n=60) . . . . . Applying LTAtransformInterp (resample_type 1) writing to /Volumes/Macintosh/freesurfer/Kontrollen//average/tmp/make_average_vol-tmp-15056/orig-A2/WE.mgh... ERROR: failure writing /Volumes/Macintosh/

Re: [Freesurfer] make_average_subject

it depends whether you want things in a coordinate system that is more anatomically accurate (.m3z) or more of a true "Talairach" one (talaraich.xfm) On Thu, 11 Aug 2011, Antonella Kis wrote: Hi Bruce, Many thanks again for your help. So just to make sure that I understood corect: is bett

[Freesurfer] make_average_subject

Hi Bruce, Many thanks again for your help. So just to make sure that I understood corect: is better to use the talairach.m3z win my make_average_subject? I was reading that the  talairach coordinate is based on talairach.xfm (unless changed with --xform) so your suggestion was to change it to ta

Re: [Freesurfer] make_average_subject error

Hi Leo, check to see if that subject's analysis is up-to-date. This usually happens when it was only partially re-run. doug leonardo kay wrote: > Hi all > > Could anyone help me with this error: > > MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 > i=5A595959, in_array_size=13

[Freesurfer] make_average_subject error

Hi all Could anyone help me with this error: MRISreadAnnotationIntoArray: vertex index out of range: 1499028058 i=5A595959, in_array_size=133467 annot file: /home/virtualuser/apps/freesurfer/subjects/s1/surf/../label/lh.aparc.annot This appeared after trying to average my subject data. It says

Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz

z name as T1.mgz. > > Thanks in advance > Best > JLH > > -Original Message- > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: Monday, June 13, 2011 11:01 PM > To: t...@ms36.hinet.net > Cc: freesurfer > Subject: Re: [Freesurfer] make_av

Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz

Do you mean your individual subject after running through FS has a file called t1.mgz and not T1.mgz? Something is definitely wrong there. Can you send the log file? doug t...@ms36.hinet.net wrote: > > Dear FS experts, > I use FS5.1 and previous data run on other machine. When I try to > make_aver

Re: [Freesurfer] make_average_subject error in T1.mgz and t1.mgz

what type of operating system are you using? On Sat, 11 Jun 2011 t...@ms36.hinet.net wrote: >

Dear FS experts,
I use FS5.1 and previous data run on > other machine. When I try to make_average_subjects program, I get error > message that it can not get T1.mgz data from subject folder. Wh

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