Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

R: Re: report a bug
by salvatoreandrea.92＠libero.it 30 Nov '15

30 Nov '15

I have around 2 Gb of total RAM. Isn't that sufficient to run recon-all? If it is not, do you know whether there is a way to split up the process? ----Messaggio originale---- Da: theniels(a)gmail.com Data: 27-nov-2015 17.24 A: "salvatoreandrea.92(a)libero.it"<salvatoreandrea.92(a)libero.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] report a bug Hi - sounds like it's running out of memory and getting killed. How much RAM do you have? On Thu, Nov 26, 2015 at 1:21 PM, salvatoreandrea.92(a)libero.it <salvatoreandrea.92(a)libero.it> wrote: Hi! - I am using Ubuntu 14.4 (trusty). - This is my subject directory: /home/salvatore/freesurfer/subjects - This is the output of which recon-all (that is the tool I am trying to use): /home/salvatore/freesurfer/bin/recon-all - The command line that I run is recon-all -s /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis -i /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis/T1.nii.gz -all Following the error that I got after 12 hours of processing: sysname Linux hostname salvatore-HP-630-Notebook-PC machine x86_64 setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects cd /home/salvatore/freesurfer/subjects/FreeSurfer_analysis/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... Killed Linux salvatore-HP-630-Notebook-PC 3.19.0-33-generic #38~14.04.1-Ubuntu SMP Fri Nov 6 18:17:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FreeSurfer_analysis exited with ERRORS at gio 26 nov 2015, 12.42.40, CET Could you please help me to fix this problem? I tried to ran it again in an other terminal, without succeding...Thank you Best, Salvatore _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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error in mri_glmfit-sim using a per-vertex regressor
by Carme Uribe Codesal 30 Nov '15

30 Nov '15

Dear FreeSurfer users, I am trying to add a per-vertex regressor in my general lineal model (a cortical thickness analysis with the white matter-grey matter contrast parameter as regressor). I have no problems with the command line mri_glmfit: mri_glmfit --y rh.cth_corr_MMSE.mgh --fsgd cth_corr_MMSE.fsgd dods --C PDcorr.mtx --pvr rh.wgc_corr_MMSE.mgh --surf fsaverage rh --cortex --glmdir rh.cth_corr_MMSE.glmdir But when I try to run mri_glmfit-sim I think it doesn't consider the regressor (mri_glmfit-sim --glmdir lh.cth_corr_MMSE.glmdir/ --cache 1.3 abs) because I get this warning: *WARNING: unrecognized mri_glmfit cmd option --pvr* *WARNING: unrecognized mri_glmfit cmd option rh.wgc_corr_MMSE.mgh* How can I run the simulation with the regressor? Thank you very much for your help, Carme

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recon-all with more than 10 inputs
by 董昊铭 30 Nov '15

30 Nov '15

Dear freesurfer exports, I am trying to recon more than 10 T1 scans from a single subject, but something went wrong. I have converted all T1 nifti files into mgz format into mri/orig directory with following names: 001.mgz 002.mgz ��. 010.mgz 011.mgz�� But when I run the command: ��recon-all �Cs ${subjec} �Cautorecon1 �Cnotal�Ccheck �Cclean-bm �Cgcut �C no-isrunning -noappend��, it seems that recon-all only recognizes the files with names 01*.mgz(i.e. 0013.mgz), the 00*.mgz(i.e. 001.mgz) files failed to be processed. Once I change the files name to ��001.mgz 002.mgz ��. 0010.mgz 0011.mgz��, the 00*. mgz(i.e. 001.mgz) are able to be recognized, but the 001*.mgz(i.e. 0013.mgz) files failed. How should I deal with this to make all files recognized? Sincerely, Dong Haoming

4 5

long run fails for new time-point when removing a tpt that was added with -addtp option
by Bishesh Khanal 30 Nov '15

30 Nov '15

Hello, I had run a longitudinal run by creating a base template with a set of time-point scans (tpts). I wanted to add a new tpt (say new1) without recreating the base template, hence I used the option -addtp in the recon-all -long run. Later on, I no longer needed the results of the long run for new1. So I removed the relevant directories for new1 (i.e. new1 and new1.long.baseid). Now I have another tpt (say new2) for which I want a -long run without recreating the base template. So I did the same thing as before i.e. first a cross run for new2 (which worked fine) and then a long-run with -addtp option. However, the long-run for new2 failed with an error that it cannot find $SUBJECTS_DIR/new1/mri/norm.mgz I realize that although I had removed the relevant directories of new1, it is still listed in the file $SUBJECTS_DIR/baseid/base-tps. However, I do not understand why norm.mgz of new1 is needed by recon-all for a long run on new2 when I did not want FreeSurfer to use either of new1 or new2 to recreate the base. Ideally, I would want to run long run on new1 and new2 under identical conditions. In other words, I do not want long-run on new2 tpt to require results from long run on new1 tpt. Should it not be the expected behaviour when I am not using new1 and/or new2 to create the base template ? And, is there a way to do achieve what I want to without manually deleting the new1 from the list in the file $SUBJECTS_DIR/baseid/base-tps ? P.S. Initially, the -addtp option had not worked and I had to do the following to make it work: The FreeSurfer version: 5.3.0. Getting around a know bug. in recon-all in the following block (around line 6148) if ( ! $found_tpNid ) then echo "ERROR: $tpNid is not in ${longbasedir}/${BaseSubjsListFname}" echo "" exit 1 endif replaced the first line (if statement) with: if ( ! $found_tpNid && ! $DoAddTp ) then

2 1

Re: [Freesurfer] ERROR: Invalid FreeSurfer license key
by Neda Mohammadi 29 Nov '15

29 Nov '15

Dear Zeke, Hi, My problem was solved, I had 2 .license files that both of them were hidden, it is my fault, sorry. :( *Best Regards,* *Neda*

1 0

FS v.6.0
by Thục Trinh 28 Nov '15

28 Nov '15

Hello Freesurfer experts, I used recon-all command for all my subject by FS v.5.3. But now I decide to upgrade to FS v.6 to eliminate some segmentation errors. The pial errors still appear on the new output of FS v.6 Can I replace the braimask.mgz of FS v.6 by the brainmask.mgz of FS v.5.3 (that been already fixed) to fixed all the pial errors, Have a nice day, Trinh

2 1

problem with cvs_avg35 option in tracula
by Alena Piovar 28 Nov '15

28 Nov '15

Dear Freesurfer experts, I tried to run tracula using cvs registration options (registration to MNI works for me well), but the -prep script crushed, when using cvs_avg35 option. I double checked the configuration file and it seems ok to me. After trying several times, I am still not able to figure out what the problem exactly is. The trac-all.log file is attached. I will be very thankful for any advice or help. Best Alena

1 0

Re: [Freesurfer] ERROR: Invalid FreeSurfer license key
by zkaufman＠nmr.mgh.harvard.edu 28 Nov '15

28 Nov '15

Hello Neda, Hello Neda, Can you please send me an email with a copy of your .license file as an attachment? *Please send it to my direct email address* and not to the Freesurfer support list. I will take a look and send you a valid license file if necessary. -Zeke > Hi Bruce, > > I'm sure about it, but I get the error. > > *Best Regards,* > *Neda* > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] ERROR: Invalid FreeSurfer license key
by Neda Mohammadi 27 Nov '15

27 Nov '15

Hi Bruce, I'm sure about it, but I get the error. *Best Regards,* *Neda*

1 0

report a bug
by salvatoreandrea.92＠libero.it 27 Nov '15

27 Nov '15

Hi! - I am using Ubuntu 14.4 (trusty). - This is my subject directory: /home/salvatore/freesurfer/subjects - This is the output of which recon-all (that is the tool I am trying to use): /home/salvatore/freesurfer/bin/recon-all - The command line that I run is recon-all -s /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis -i /home/salvatore/Tirocinio/Dati_DTI/DTI1/FreeSurfer_analysis/T1.nii.gz -all Following the error that I got after 12 hours of processing: sysname Linux hostname salvatore-HP-630-Notebook-PC machine x86_64 setenv SUBJECTS_DIR /home/salvatore/freesurfer/subjects cd /home/salvatore/freesurfer/subjects/FreeSurfer_analysis/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /home/salvatore/freesurfer/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... Killed Linux salvatore-HP-630-Notebook-PC 3.19.0-33-generic #38~14.04.1-Ubuntu SMP Fri Nov 6 18:17:28 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s FreeSurfer_analysis exited with ERRORS at gio 26 nov 2015, 12.42.40, CET Could you please help me to fix this problem? I tried to ran it again in an other terminal, without succeding...Thank you Best, Salvatore

2 1

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Freesurfer November 2015