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 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 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 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 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_

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 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

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

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. When I check my dataset, actually it has t1.mgz rather than T1.mgz. how could I change the setting fr

Re: [Freesurfer] make_average_subject error about limit

You probably have an older version that does not recoginze --cortex. Try --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label instead Feng-Xian wrote: Hi, Thank you for your response! I solve this problem of mris_preproc. The next step is to do mri_glmfit. And, when I type the followi

Re: [Freesurfer] make_average_subject error about limit

Hi, Thank you for your response! I solve this problem of mris_preproc. The next step is to do mri_glmfit. And, when I type the following command: mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir lh.no

Re: [Freesurfer] make_average_subject error about limit

Is there a space between "--" and "hemi"? caching is just a way to speed some analyses by pre-smoothing and sampling to the standard space. doug Feng-Xian wrote: Hi, I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir. Then, I make a FSGD file an

Re: [Freesurfer] make_average_subject error about limit

Hi, I copied the default average subject from $FREESURFER_HOME/subjects dir to my analysis dir. Then, I make a FSGD file and some contrast matrices and put them into my analysis dir. After that, I start to run group analysis. But, when I type the following commands: mris_preproc --fsg

Re: [Freesurfer] make_average_subject error about limit

You don't *have to* to run make_average_subject to do your analysis, only if you want to view the results on a map with the curvature patterns averaged over your subjects. As for the limit error, how old is your version of freesurfer? That line was removed about 1.5 years ago... doug Feng-Xia

Re: [Freesurfer] make_average_subject error about limit

Feng-xian, I should also mention that i dont think creating your own average subject will solve the problem you describe, where you need to work with three levels in your group. for that, you wont be able to use qdec, but will need to run things manually. these pages give examples: http://surfe

Re: [Freesurfer] make_average_subject error about limit

Feng-Xian, It appears that you do not have permission on your system to change the limits. So you will have to edit the scripts make_average_volume, make_average_surface and make_average_subject to comment out the 'limit' line, so that it looks like this: #limit descriptors unlimited Nick On

[Freesurfer] make_average_subject error about limit

Hi, I have a problem with make_average_subject. After running all commands (including ln -s $FREESURFER_HOME/subjects/fsaverage and recon-all -s -qcache for all my subjects) about running QDEC, I found that QDEC could not analysis my group. Because the group have 1 factor and three level

[Freesurfer] make_average_subject error about limit

Hi, I have a problem with make_average_subject. After running all commands about running QDEC, I found that QDEC could not analysis my group. Because the group I want to analysis have 1 factor and three levels, QDEC can't run. So, I want to change the method of analysis from QDEC to FSGD.

Re: [Freesurfer] Make_average_subject error

From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Wed 5/9/2007 6:21 PM To: Furlong, Carolyn Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Make_average_subject error you may be using a version that does not have

Re: [Freesurfer] Make_average_subject error

take per subject? Best wishes Carolyn From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Wed 5/9/2007 6:21 PM To: Furlong, Carolyn Cc: Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Make_average_subject error you may be using a version that does not have

Re: [Freesurfer] Make_average_subject error

you may be using a version that does not have this option. Try using these doug ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_subject ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface Furlong, Carolyn wrote: Hi all, I tried runn

Re: [Freesurfer] Make_average_subject error

I have been able to run it with --no-symlink (the flag has to go last), but I get errors like this: mris_make_average_surface: could not read surface file /Volumes/data/NL-GCS/subjects/freesurfer_3.0.1/GCS_adults/--no-symlink/surf/rh.sphere.reg Thanks. Anthony Furlong, Carolyn wrote: Hi

[Freesurfer] Make_average_subject error

Hi all, I tried running it again with --no-symlink but this error came up ERROR: Flag --no-symlink unrecognized. any advice? Best wishes Carolyn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listi

[Freesurfer] Make_average_subject error

Hi all I have run the script make_average_subject and the error message at the end is: ln: creating symbolic link `rh.sphere' to `rh.sphere.reg': Operation not permitted only rh* files have been created. Can you help? Best wishes Carolyn ___ Frees

Re: [Freesurfer] make_average_subject error?

Title: Re: [Freesurfer] make_average_subject error? Hi Doug, I changed the flags to “efxv” as you recommend, and here is the output for make_average_subject, make_average_volume and make_average_surface. The script doesn’t seem to be accepting my command line arguments. I am using the current

Re: [Freesurfer] make_average_subject error?

Try editing those scripts so that the first line is: #!/bin/tcsh -efxv ie, adding "xv" This turns on all kinds of debugging Brian Schweinsburg, Ph.D. wrote: Re: [Freesurfer] make_average_subject error? Hi Doug, The same thing happens when I try to run them separately. I

Re: [Freesurfer] make_average_subject error?

Title: Re: [Freesurfer] make_average_subject error? Hi Doug, The same thing happens when I try to run them separately. It exits to the prompt with no messages. Brian -- Brian C. Schweinsburg, Ph.D. Assistant Adjunct Professor of Psychiatry University of California, San Diego Office: 858-552

Re: [Freesurfer] make_average_subject error?

"freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] make_average_subject error? try running it with --debug and send us the output Brian Schweinsburg, Ph.D. wrote: Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volum

Re: [Freesurfer] make_average_subject error?

xit 0" Brian > From: Doug Greve <[EMAIL PROTECTED]> > Date: Mon, 26 Sep 2005 16:40:48 -0400 > To: "Brian Schweinsburg, Ph.D." <[EMAIL PROTECTED]> > Cc: "freesurfer@nmr.mgh.harvard.edu" > Subject: Re: [Freesurfer] make_average_subject error? &

Re: [Freesurfer] make_average_subject error?

try running it with --debug and send us the output Brian Schweinsburg, Ph.D. wrote: Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh wit

[Freesurfer] make_average_subject error?

Hi Folks, I tried running the latest make_average_subject script (and the make_average_surface/volume scripts) using the expected command line syntax and after hitting enter it immediately exits to the csh without error, but does not produce anything. make_average_subject --subjects SC010 SC011 S