[Freesurfer] seed generation for tractography
Dear FS experts, I have created some seed files and wanted to ask you if everything is fine with this procedure. After using recon-all -subject xy -i xy.nii.gz -all, I labelled my files with mri_binarize --match ID --i aparc.a2009s+aseg.mgz --o label.nii.gz Then I used bbregister and mri_label2vol to map these files into diffusion space. These were the commands: - bbregister --s xy --mov xy/mri/b0_brain.nii.gz --reg xy/mri/registration2b0.dat --dti --init-fsl - mri_label2vol --seg label.nii.gz --temp b0_brain.nii.gz --reg registration2b0.dat --o label_dwi_seed.nii.gz I attach one of such dwi_seed file. Can please check if it looks ok? Thanks a lot for your help André left_caudate_dwi_seed.nii.gz Description: left_caudate_dwi_seed.nii.gz ___ 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] qdec - Generate stats data table
Dear FS experts,I am trying to generate my stats data tables with QDEC -after successfully loading my data table- and come across the following error.Any recommendations would be greatly appreciated.Thank you in advancePabloData table loading completed successfully. SUBJECTS_DIR is '/Volumes/NEW_VOLUME/GBS' mkdir -p /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/ -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files Building the table.. Writing the table to /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/wmparc.volume.stats.dat --statsfile=wmparc.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files ERROR: The stats file /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files ___ 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] Issue with converting aseg.mgz file to .nii file
How are you generating the stats? The aseg.stats file uses partial volume correction... On 08/03/2015 04:48 PM, Jonathan Plasencia wrote: That is partly correct. The nii is not matching the stats file (which it is my understanding the stats file is based off the mgz file. If this is the case then yes to your first question). I'll send a mgz file and its stats file directly to your personal email in a minute: fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu Best, Jon On Mon, Aug 3, 2015 at 1:18 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: and you are saying that aseg.nii does *not* match the voxel counts in aseg.mgz? That is surprising. Can you email me the aseg.mgz? On Mon, 3 Aug 2015, Jonathan Plasencia wrote: I've given it a try in which I do not include --out_orientation RAS for writting an nii file (see output below). In doing so the new aseg.nii file appears to be the exact same as the original nii files I created (i.e. the number of voxels for a given segmentation ID did not change between the old and new nii file and neither of these are matching the stats file). Do you have another suggestion for fixing this? I ask because some of the smaller structures can have up to a 30% change in the number of voxels representing a given structure (comparing the nii file to the stats file). r500711$ mri_convert aseg.mgz aseg.nii mri_convert aseg.mgz aseg.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to aseg.nii... On Fri, Jul 31, 2015 at 2:31 PM, Jonathan Plasencia jplas...@asu.edu mailto:jplas...@asu.edu wrote: Ok, I will give this a look. Thank you everyone.Best, Jon cheers Bruce On Fri, 31 Jul 2015, Jonathan Plasencia wrote: This is what we did from terminal: mri_convert aseg.mgz aseg.nii --out_orientation RAS mri_convert aseg.mgz aseg.nii --out_orientation RAS $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Setting output orientation to RAS Reslicing using trilinear interpolation writing to aseg.nii... ** I ran this command from within the subject's mri folder. Should we try this without --out_orientation RAS ? Best, Jonathan Plasencia Graduate Student NSF Graduate Research Fellow School of Biological and Health Systems Engineering Arizona State University Email: jplas...@asu.edu mailto:jplas...@asu.edu Phone: (480)861-7017 tel:%28480%29861-7017 On Fri, Jul 31, 2015 at 12:54 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: why are you specifying the output orientation? That is probably causing resampling On Fri, 31 Jul 2015, Jonathan Plasencia wrote: We are using the following line: mri_convert aseg.mgz aseg.nii --out_orientation RAS Best, Jonathan Plasencia Graduate Student NSF Graduate Research Fellow School of Biological and Health Systems Engineering Arizona State University Email: jplas...@asu.edu mailto:jplas...@asu.edu Phone: (480)861-7017 tel:%28480%29861-7017 On Fri, Jul 31, 2015 at
Re: [Freesurfer] Issue with converting aseg.mgz file to .nii file
yes, I think that was the issue and it is now sorted out Bruce On Tue, 4 Aug 2015, Douglas N Greve wrote: How are you generating the stats? The aseg.stats file uses partial volume correction... On 08/03/2015 04:48 PM, Jonathan Plasencia wrote: That is partly correct. The nii is not matching the stats file (which it is my understanding the stats file is based off the mgz file. If this is the case then yes to your first question). I'll send a mgz file and its stats file directly to your personal email in a minute: fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu Best, Jon On Mon, Aug 3, 2015 at 1:18 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: and you are saying that aseg.nii does *not* match the voxel counts in aseg.mgz? That is surprising. Can you email me the aseg.mgz? On Mon, 3 Aug 2015, Jonathan Plasencia wrote: I've given it a try in which I do not include --out_orientation RAS for writting an nii file (see output below). In doing so the new aseg.nii file appears to be the exact same as the original nii files I created (i.e. the number of voxels for a given segmentation ID did not change between the old and new nii file and neither of these are matching the stats file). Do you have another suggestion for fixing this? I ask because some of the smaller structures can have up to a 30% change in the number of voxels representing a given structure (comparing the nii file to the stats file). r500711$ mri_convert aseg.mgz aseg.nii mri_convert aseg.mgz aseg.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to aseg.nii... On Fri, Jul 31, 2015 at 2:31 PM, Jonathan Plasencia jplas...@asu.edu mailto:jplas...@asu.edu wrote: Ok, I will give this a look. Thank you everyone.Best, Jon cheers Bruce On Fri, 31 Jul 2015, Jonathan Plasencia wrote: This is what we did from terminal: mri_convert aseg.mgz aseg.nii --out_orientation RAS mri_convert aseg.mgz aseg.nii --out_orientation RAS $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from aseg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Setting output orientation to RAS Reslicing using trilinear interpolation writing to aseg.nii... ** I ran this command from within the subject's mri folder. Should we try this without --out_orientation RAS ? Best, Jonathan Plasencia Graduate Student NSF Graduate Research Fellow School of Biological and Health Systems Engineering Arizona State University Email: jplas...@asu.edu mailto:jplas...@asu.edu Phone: (480)861-7017 tel:%28480%29861-7017 On Fri, Jul 31, 2015 at 12:54 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: why are you specifying the output orientation? That is probably causing resampling On Fri, 31 Jul 2015, Jonathan Plasencia wrote: We are using the following line: mri_convert aseg.mgz aseg.nii --out_orientation RAS Best, Jonathan Plasencia Graduate Student NSF Graduate Research Fellow School of Biological and Health Systems Engineering Arizona State University Email: jplas...@asu.edu mailto:jplas...@asu.edu Phone: (480)861-7017
Re: [Freesurfer] qdec - Generate stats data table
Have you looked in /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats to see if there might be a problem? On 08/04/2015 05:43 AM, pablo najt wrote: Dear FS experts, I am trying to generate my stats data tables with QDEC -after successfully loading my data table- and come across the following error. Any recommendations would be greatly appreciated. Thank you in advance Pablo Data table loading completed successfully. SUBJECTS_DIR is '/Volumes/NEW_VOLUME/GBS' mkdir -p /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/ -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files Building the table.. Writing the table to /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/wmparc.volume.stats.dat --statsfile=wmparc.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files ERROR: The stats file /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files ___ 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] recon-all exited with errors
Hello, I am very new to freesurfer who have been using SPM and FSL, and just started doing individual subject analysis. I already had an error message on recon-all step. I am using: Vertualbox, OS is RedHat 64-bit I am using bash (I prefer to do so) so I am not in tsch shell. The recon-all process was terminated with error but not sure exactly what the error was even I looked at the recon-all.log file which is attached to this e-mail. According to the line of script, there should be a file called 'talairach.xfm in /mri/transforms folder but I see only the folder called 'bak' which is empty. Please advise what is the exact error is and how to solve this problem. Thank you so much for your help in advance. Hisako * fsuser@xubuntu-VirtualBox:/media/sf_shared_folder/CAE_MRI$ recon-all -i CAE_2_1_T1.nii -subject CAE_2_1 -all WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /media/sf_shared_folder Actual FREESURFER_HOME /usr/local/freesurfer Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux /media/sf_shared_folder/CAE_2_1 mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz... # #@# MotionCor Tue Aug 4 10:04:50 EDT 2015 Found 1 runs /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz /media/sf_shared_folder/CAE_2_1 mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) Original Data has (0.976562, 0.976562, 1) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /media/sf_shared_folder/CAE_2_1/mri/orig.mgz... mri_add_xform_to_header -c /media/sf_shared_folder/CAE_2_1/mri/transforms/talairach.xfm /media/sf_shared_folder/CAE_2_1/mri/orig.mgz /media/sf_shared_folder/CAE_2_1/mri/orig.mgz INFO: extension is mgz # #@# Talairach Tue Aug 4 10:05:06 EDT 2015 /media/sf_shared_folder/CAE_2_1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux recon-all -s CAE_2_1 exited with ERRORS at Tue Aug 4 10:05:13 EDT 2015 For more details, see the log file /media/sf_shared_folder/CAE_2_1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting fsuser@xubuntu-VirtualBox:/media/sf_shared_folder/CAE_MRI$ recon-all.log Description: recon-all.log ___ 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] Dimension mismatch between mask and run
I'm not sure, but it may be that there are some files that are nii and others that are nii.gz. Eg, ls -tl /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/015/masks/ total 1248 -rw-rw 1 arodthom roffmagp 3579 Aug 3 18:06 brain.e3.nii.gz -rw-rw 1 arodthom roffmagp 5383 Aug 3 18:06 brain.nii.gz -rw-rw 1 arodthom roffmagp 606560 Mar 16 11:02 brain.e3.nii -rw-rw 1 arodthom roffmagp 606560 Mar 16 11:02 brain.nii The nii.gz are newer but I think selxavg3-sess will use the nii files, which have probably not been updated. Try deleting the same-named nii files On 08/03/2015 06:32 PM, Rodriguez-Thompson, Anais wrote: Hi Freesurfer experts, For a data set of n=100, selxavg3 is erroring out on 10 subjects (GDDA086, 88, 89, 91, 93, 94, 95, 96, 97, and 98). It says ERROR: dimension mismatch between mask and 1th run. Do you know why freesurfer is having trouble with these subjects in particular, and how I can avoid this error? Thanks for your help, Anais Below is the terminal window output: -- selxavg3-sess logfile is /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_050514-150803173934.log -- preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_050514 -nolog -- preproc-sess logfile is /dev/null -- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ arodthom setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_050514 -nolog Mon Aug 3 17:39:35 EDT 2015 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 fmcpr mask 1 brain GDDA098 Template - mktemplate-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile -nolog -update Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Mon Aug 3 17:39:36 EDT 2015 Detected input format at nii GDDA098 Update not needed Run: 015 Mon Aug 3 17:39:36 EDT 2015 GDDA098 015 Update not needed Run: 016 Mon Aug 3 17:39:36 EDT 2015 GDDA098 016 Update not needed Run: 017 Mon Aug 3 17:39:36 EDT 2015 GDDA098 017 Update not needed Mon Aug 3 17:39:36 EDT 2015 mktemplate-sess completed GDDA098 Mask mkbrainmask-sess -maskstem brain -fsd bold -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Mon Aug 3 17:39:36 EDT 2015 WARNING: multiple formats found for template USING: template.nii.gz GDDA098 Update not needed for session-level mask WARNING: multiple formats found for 015/template USING: 015/template.nii.gz GDDA098 Update not needed for run 015 mask GDDA098 Update not needed for run 015 meanval WARNING: multiple formats found for 016/template USING: 016/template.nii.gz GDDA098 Update not needed for run 016 mask GDDA098 Update not needed for run 016 meanval WARNING: multiple formats found for 017/template USING: 017/template.nii.gz GDDA098 Update not needed for run 017 mask GDDA098 Update not needed for run 017 meanval Mon Aug 3 17:39:37 EDT 2015 mkbrainmask-sess done GDDA098 Registration - register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update -- register-sess logfile is /dev/null -- Mon Aug 3 17:39:37 EDT 2015 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Mon Aug 3 17:39:37 EDT 2015 Run: 015 Mon Aug 3 17:39:37 EDT 2015 WARNING: multiple formats found for
Re: [Freesurfer] Issue with Optseq2 download
I cannot replicate the problem, but I'm inside the surfer domain. Have you tried from another computer? We had these kinds of problems before and the problem was a firewall on the side of the person trying to do the download. doug On 08/03/2015 06:36 PM, Perugini, Alessandra wrote: Hi, I am trying to download the Optseq software from this link: /http://surfer.nmr.mgh.harvard.edu/optseq/ However once I click Download, an error occurs and the page does not load. I have tried a number of times. I have a Mac OS X 10.10.4 Anybody with the same problem? Any suggestions? Thanks, Alessandra /Alessandra Perugini, PhD/ /Postdoctoral Scholar / /Semel Institute for Neuroscience Human Behavior/ /University of California, Los Angeles/ IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer. ___ 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] qdec problem
Dear suffers Now, I’m running the group analysis using qdec as a beginner. 2 groups, 4patients per each group.. after successful data table loading, I choosed 'Generate Stats Data Tables button’ I found the error message like below,, could you help me ? thanks Hyon-Ah Data table loading completed successfully. SUBJECTS_DIR is '/Users/i_geschwind/Desktop/qdec_test' mkdir -p /Users/i_geschwind/Desktop/qdec_test/qdec/stats_tables/ -- asegstats2table --common-segs --meas volume --tablefile /Users/i_geschwind/Desktop/qdec_test/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects CDPAD02WJD_recon CDPAD09HOH_recon CDPAD26LJC_recon CDPAD28_KEJ2419486 CDPcon02_recon CDPcon03_recon CDPcon04_recon CDPcon05_recon SUBJECTS_DIR : /Users/i_geschwind/Desktop/qdec_test Parsing the .stats files ERROR: The stats file /Users/i_geschwind/Desktop/qdec_test/CDPAD02WJD_recon/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files ERROR: In /usr/pubsw/packages/KWWidgets/CVS-7Aug2010/src/KWWidgets/vtkKWTkUtilities.cxx, line 230 vtkKWQdecApp (0x6108820): Script: vtkTemp2 GenerateStatsDataTables Returned Error on line 1: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /Users/i_geschwind/Desktop/qdec_test/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects CDPAD02WJD_recon CDPAD09HOH_recon CDPAD26LJC_recon CDPAD28_KEJ2419486 CDPcon02_recon CDPcon03_recon CDPcon04_recon CDPcon05_recon Stack trace: Uncaught exception: command failed: asegstats2table --common-segs --meas volume --tablefile /Users/i_geschwind/Desktop/qdec_test/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects CDPAD02WJD_recon CDPAD09HOH_recon CDPAD26LJC_recon CDPAD28_KEJ2419486 CDPcon02_recon CDPcon03_recon CDPcon04_recon CDPcon05_recon while executing vtkTemp2 GenerateStatsDataTables ___ 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] ThickAvg of specific structures
Hi, If I am only interested in the gm thickness (ThickAvg) of a specific structure/s (e.g. precentral) is it sufficient to only QC these specific structures/s or does the wm and pial surface need to be accurate across the entire hemisphere for the accurate determination of gm thickness of the specified structure/s? Thanks, P ___ 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] ThickAvg of specific structures
Just doing those structures should be fine Bruce On Aug 4, 2015, at 10:46 PM, prasser pras...@zoho.com wrote: Hi, If I am only interested in the gm thickness (ThickAvg) of a specific structure/s (e.g. precentral) is it sufficient to only QC these specific structures/s or does the wm and pial surface need to be accurate across the entire hemisphere for the accurate determination of gm thickness of the specified structure/s? Thanks, P ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] qdec - Generate stats data table
thanks! Date: Tue, 4 Aug 2015 15:01:43 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec - Generate stats data table You can just run recon-all with the -wmparc flag. It should be pretty quick, less than 30 min or soo On 08/04/2015 12:04 PM, pablo najt wrote: Thank you this subject had a zip copy of the wmparc.stats Now I am missing this file from another subject. Do I need to run recon-all from start or is there a shortcut for getting this file? Thanks Doug. Pablo Date: Tue, 4 Aug 2015 11:42:43 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec - Generate stats data table Have you looked in /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats to see if there might be a problem? On 08/04/2015 05:43 AM, pablo najt wrote: Dear FS experts, I am trying to generate my stats data tables with QDEC -after successfully loading my data table- and come across the following error. Any recommendations would be greatly appreciated. Thank you in advance Pablo Data table loading completed successfully. SUBJECTS_DIR is '/Volumes/NEW_VOLUME/GBS' mkdir -p /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/ -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files Building the table.. Writing the table to /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/wmparc.volume.stats.dat --statsfile=wmparc.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files ERROR: The stats file /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files ___ 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
Re: [Freesurfer] Weird Freesurfer results
Hi Brent are you saying you just multiplied the gray matter intensities by some scale factor (1)? Bruce On Tue, 4 Aug 2015, Brent Womble wrote: Hi everyone, I've been making synthetic brains to test how Freesurfer handles various structural changes. One of the changes I'm testing is increased density (like in VBM). To simulate increased density, I used a spherical Gaussian multiplication kernel, with a radius of 20 voxels. I centered this kernel at a point in the right superior frontal gyrus and masked the changes to grey matter using the segmentation output from SPM12. Here is an example, a difference image (synth.nii - pre.nii): [IMAGE] Around that area, Freesurfer didn't detect a change (as I expected): Inline image 2 Original in red and blue, synthetic in pink and light blue. The problem is that the longitudinal streams in Freesurfer found a bunch of changes in random parts of the brain. We looked at the recons for each subject individually, and saw some noise around the clusters that were significant in the two-stage model. This doesn't make sense, because the actual voxels were exactly the same in that region. For example: [IMAGE] I redid the recon-all with the -nonormalization flag. It didn't fix the problem. For example (same subject as above): [IMAGE] I thought it might have been an issue caused by my increased density method, so I ran it again, this time with the kernel centered in the cerebellum (still masked to grey matter). I still got weird changes in unrelated parts of the cortex. For example (same subject as above): [IMAGE] Note: light blue/red and blue/red are reversed in this one, just because of the order I loaded it in Freeview. In summary, Freesurfer found a bunch of weird changes that were nowhere near the changes I actually made. Where should I go from here? -Brent ___ 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] Weird Freesurfer results
Yes. Here is the MATLAB script:
for i = [1:20]%Load the original image and gray matter
maskraw=load_nii([pwd,'/',
num2str(i), '/pre.nii'])a=single(squeeze(raw.img));
c1_raw=load_nii([pwd,'/', num2str(i),
'/c1pre.nii']);c1=squeeze(c1_raw.img);%Mask
is gray around edges. Threshold to make it binaryc1(c10.1)=1;%Convert mask
to logicalc1=logical(c1);
%%Generate a 3D gaussian kernel%Specify the origin, size, and intensity of
the kernelk_origin=origins(i,:); %origins is an i by 3 vector to store all
coordinatesk_size=20;k_intensity=100;
k=1-fspecial3
http://www.mathworks.com/matlabcentral/fileexchange/4917-skeleton-in-3d/content/fspecial3.m
('gaussian',k_size).*k_intensity;k(k0)=0;
%Expand the kernel to the size of the original imagepadsize_pre=k_origin -
(k_size/2);padsize_post=size(a) - k_origin - (k_size/2);
k=padarray(k,padsize_post,1,'post');k=padarray(k,padsize_pre,1,'pre');
%Restrict the kernel to the gray maskb=k.*c1;b(~c1)=1;
%%Apply the kernel to the original imagec=b.*a;
%Write to .niiraw.img=c;save_nii(raw,[pwd,'/', num2str(i),
'/dense-synth.nii']);end
On Tue, Aug 4, 2015 at 11:52 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Brent
are you saying you just multiplied the gray matter intensities by some
scale factor (1)?
Bruce
On Tue, 4 Aug 2015, Brent Womble wrote:
Hi everyone,
I've been making synthetic brains to test how Freesurfer handles various
structural changes.
One of the changes I'm testing is increased density (like in VBM). To
simulate increased density, I used a spherical Gaussian multiplication
kernel, with a radius of 20 voxels. I centered this kernel at a point in
the right superior frontal gyrus and masked the changes to grey matter
using
the segmentation output from SPM12.
Here is an example, a difference image (synth.nii - pre.nii):
[IMAGE]
Around that area, Freesurfer didn't detect a change (as I expected):
Inline image 2
Original in red and blue, synthetic in pink and light blue.
The problem is that the longitudinal streams in Freesurfer found a bunch
of
changes in random parts of the brain.
We looked at the recons for each subject individually, and saw some noise
around the clusters that were significant in the two-stage model. This
doesn't make sense, because the actual voxels were exactly the same in
that
region. For example:
[IMAGE]
I redid the recon-all with the -nonormalization flag. It didn't fix the
problem. For example (same subject as above):
[IMAGE]
I thought it might have been an issue caused by my increased density
method,
so I ran it again, this time with the kernel centered in the cerebellum
(still masked to grey matter). I still got weird changes in unrelated
parts
of the cortex. For example (same subject as above):
[IMAGE]
Note: light blue/red and blue/red are reversed in this one, just because
of
the order I loaded it in Freeview.
In summary, Freesurfer found a bunch of weird changes that were nowhere
near
the changes I actually made.
Where should I go from here?
-Brent
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Re: [Freesurfer] bbregister --12?
Yes, it is for 12dof. It is not hidden for any particular purpose (except maybe that I'm lazy). In general, I don't think it is a good idea to use 12 or 9 dof unless you have an explicit reason to. On 08/04/2015 01:54 PM, Perea Camargo, Rodrigo Dennis wrote: Hi all, I am using a previous script to update a pipeline for pre-processing diffusion data. My objective related to this question is the (what I think is a hidden) argument “- -12” when using bbregister (v. 1.49.2.3 FreeSurfer 5.3). Will this denote 12 degrees of freedom for my registration? If so, why is this argument hidden (not in the manual or --help) and what are your insights when registering diffusion data to the Freesurfer T1 image? Should I keep 12dof or just do a simple rigid body registraion (e.g. 6 dof) Thanks in advance for your response, Rodrigo ___ 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] Weird Freesurfer results
What you really want to simulate is an underlying geometric deformation
(like atrophy) that gets propagated through an image formation model to
create an atrophic image. I don't think multiplying the image intensities
is a good model for what you want. Atrophy doesn't look like a uniform
darkening of the gray matter.
On Tue, 4 Aug 2015, Brent Womble wrote:
Yes, I'm multiplying the image intensities by a scaling factor. Sorry if
that wasn't clear.
-Brent
On Aug 4, 2015 12:09, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Brent
a quick look and it seems that your answer is yes? You are
multiplying the image intensities by some scale factor?
Bruce
On Tue, 4 Aug 2015, Brent Womble wrote:
Yes. Here is the MATLAB script:
for i = [1:20]
%Load the original image and gray matter mask
raw=load_nii([pwd,'/', num2str(i),
'/pre.nii'])
a=single(squeeze(raw.img));
c1_raw=load_nii([pwd,'/', num2str(i),
'/c1pre.nii']);
c1=squeeze(c1_raw.img);
%Mask is gray around edges. Threshold to make
it binary
c1(c10.1)=1;
%Convert mask to logical
c1=logical(c1);
%%Generate a 3D gaussian kernel
%Specify the origin, size, and intensity of
the kernel
k_origin=origins(i,:); %origins is an i by 3
vector to store
all coordinates
k_size=20;
k_intensity=100;
k=1-fspecial3('gaussian',k_size).*k_intensity;
k(k0)=0;
%Expand the kernel to the size of the original
image
padsize_pre=k_origin - (k_size/2);
padsize_post=size(a) - k_origin - (k_size/2);
k=padarray(k,padsize_post,1,'post');
k=padarray(k,padsize_pre,1,'pre');
%Restrict the kernel to the gray mask
b=k.*c1;
b(~c1)=1;
%%Apply the kernel to the original image
c=b.*a;
%Write to .nii
raw.img=c;
save_nii(raw,[pwd,'/', num2str(i),
'/dense-synth.nii']);
end
On Tue, Aug 4, 2015 at 11:52 AM, Bruce Fischl
fis...@nmr.mgh.harvard.edu
wrote:
Hi Brent
are you saying you just multiplied the gray
matter intensities
by some scale factor (1)?
Bruce
On Tue, 4 Aug 2015, Brent Womble wrote:
Hi everyone,
I've been making synthetic brains to
test how
Freesurfer handles various
structural changes.
One of the changes I'm testing is
increased density
(like in VBM). To
simulate increased density, I used a
spherical
Gaussian multiplication
kernel, with a radius of 20 voxels. I
centered this
kernel at a point in
the right superior frontal gyrus and
masked the
changes to grey matter using
the segmentation output from SPM12.
Here is an example, a difference image
(synth.nii -
pre.nii):
[IMAGE]
Around that area, Freesurfer didn't
detect a change
(as I expected):
Inline image 2
Original in red and blue, synthetic in
pink and
light blue.
The problem is that the longitudinal
streams in
Freesurfer found a bunch of
changes in random parts of the brain.
We looked at the recons for each subject
individually, and saw some noise
around the clusters that were
significant in the
two-stage model. This
doesn't make sense, because the actual
voxels were
exactly the same in that
region. For example:
[IMAGE]
I redid the recon-all with the
-nonormalization
flag. It didn't fix the
problem. For example (same subject as
above):
[IMAGE]
Re: [Freesurfer] Dimension mismatch between mask and run
Hi Doug, Thanks for getting back to me. I tried deleting those files, and got the same error, although the terminal output looked slightly different towards the end (in terms of the compensation values). Here it is below: -- selxavg3-sess logfile is /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_050514-150804121216.log -- preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_050514 -nolog -- preproc-sess logfile is /dev/null -- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ arodthom setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_050514 -nolog Tue Aug 4 12:12:17 EDT 2015 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 fmcpr mask 1 brain GDDA098 Template - mktemplate-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile -nolog -update Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Tue Aug 4 12:12:17 EDT 2015 Detected input format at nii GDDA098 Update not needed Run: 015 Tue Aug 4 12:12:17 EDT 2015 GDDA098 015 Update not needed Run: 016 Tue Aug 4 12:12:17 EDT 2015 GDDA098 016 Update not needed Run: 017 Tue Aug 4 12:12:17 EDT 2015 GDDA098 017 Update not needed Tue Aug 4 12:12:17 EDT 2015 mktemplate-sess completed GDDA098 Mask mkbrainmask-sess -maskstem brain -fsd bold -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Tue Aug 4 12:12:17 EDT 2015 WARNING: multiple formats found for template USING: template.nii.gz GDDA098 Update not needed for session-level mask WARNING: multiple formats found for 015/template USING: 015/template.nii.gz GDDA098 Update not needed for run 015 mask GDDA098 Update not needed for run 015 meanval WARNING: multiple formats found for 016/template USING: 016/template.nii.gz GDDA098 Update not needed for run 016 mask GDDA098 Update not needed for run 016 meanval WARNING: multiple formats found for 017/template USING: 017/template.nii.gz GDDA098 Update not needed for run 017 mask GDDA098 Update not needed for run 017 meanval Tue Aug 4 12:12:18 EDT 2015 mkbrainmask-sess done GDDA098 Registration - register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update -- register-sess logfile is /dev/null -- Tue Aug 4 12:12:18 EDT 2015 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Tue Aug 4 12:12:18 EDT 2015 Run: 015 Tue Aug 4 12:12:18 EDT 2015 WARNING: multiple formats found for bold/015/template USING: bold/015/template.nii.gz Update not needed Run: 016 Tue Aug 4 12:12:18 EDT 2015 WARNING: multiple formats found for bold/016/template USING: bold/016/template.nii.gz Update not needed Run: 017 Tue Aug 4 12:12:18 EDT 2015 WARNING: multiple formats found for bold/017/template USING: bold/017/template.nii.gz Update not needed Tue Aug 4 12:12:18 EDT 2015 register-sess completed GDDA098 MC - mc-sess -fstem f -fmcstem fmcpr -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile -per-run -nolog -update Logfile is /dev/null --- /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 RunList: 015 016 017 WARNING: multiple formats found for 015/template USING: 015/template.nii.gz GDDA098 015 Update not needed WARNING: multiple formats found for
Re: [Freesurfer] cannot find qdec file
oops, sorry for the delay, thanks for the reminder. The problem is that you have a blank line at the end of your long.qdec.table.dat file. Remove the line and see if it works. doug On 08/04/2015 12:42 PM, Clara Kühn wrote: Hi Doug, did the fordoug.log file give any information about why FreeSurfer can't find my qdec file? Cheers and thanks for working on this! Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 17:16:18 Betreff: Re: [Freesurfer] cannot find qdec file can you run mris_preproc --debug --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh | tee fordoug.log and send me fordoug.log ? On 8/3/15 10:38 AM, Clara Kühn wrote: the command line is this: mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh the terminal output is this: nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. and the actual qdec file is attached. Cheers, Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24 Betreff: Re: [Freesurfer] cannot find qdec file Can you send your command line, full terminal output, and your long.qdec.table.dat file? On 8/3/15 10:31 AM, Clara Kühn wrote: ok, it can only access the file if I type ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash) but if I then use that path for the mris_preproc command I get nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48 Betreff: Re: [Freesurfer] cannot find qdec file that is probably not the full path. Try typing ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat If it says it cannot find the file, then it is not the full path. Maybe you need a forward slash (ie, /) in the beginning? On 8/3/15 10:18 AM, Clara Kühn wrote: then I get the error ERROR: cannot find scr/etsch2/kids/ct/qdec/long.qdec.table.dat I had tried that. Sorry, no luck with that. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58 Betreff: Re: [Freesurfer] cannot find qdec file you have to give it the entire path to the file On 8/3/15 10:14 AM, Clara Kühn wrote: Dear FS-experts, I want to analyze my longitudinal data with your suggested LME models and am therefore following the walkthrough by J. Bernal. I get an error though very early on when using the command mris_preproc --qdec-long qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out qdec/lh.thickness.mgh It always says ERROR: cannot find qdec/long.qdec.table.dat Yes, the walkthrough asks for an input file named just qdec.table.dat, but I haven't got that. So far in the longitudinal stream there are long.qdec.table.dat and cross.qdec.table.dat files but no simple qdec.table.dat files. So I figured I'd use the long.qdec file because FS needs to get the information about the long timepoints. But it cannot find the file, even though I see it. I've also tried copying the long.qdec file and naming it qdec.table.dat but it still doesn't find it. The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat and my SUBJECTS_DIR is scr/etsch2/kids/ct Can you help me see what I'm missing? Thanks a lot in advance, Clara ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer
[Freesurfer] [Tracula] pathstats.byvoxel.txt for between-group or correlational analyses
Dear Anastasia and Tracula experts, I would like to run between-group statistics using the pathstats.byvoxel.txt outputs. It is clear from the website how to manage the NANs. However, what would you suggest to use for between-group or correlational analyses? Is there a script/function/statistical package in tracula that can handle this kind of data? Thanks a lot, Amelia ___ 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] cannot find qdec file
Hi Doug, did the fordoug.log file give any information about why FreeSurfer can't find my qdec file? Cheers and thanks for working on this! Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 17:16:18 Betreff: Re: [Freesurfer] cannot find qdec file can you run mris_preproc --debug --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh | tee fordoug.log and send me fordoug.log ? On 8/3/15 10:38 AM, Clara Kühn wrote: the command line is this: mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh the terminal output is this: nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. and the actual qdec file is attached. Cheers, Clara - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:35:24 Betreff: Re: [Freesurfer] cannot find qdec file Can you send your command line, full terminal output, and your long.qdec.table.dat file? On 8/3/15 10:31 AM, Clara Kühn wrote: ok, it can only access the file if I type ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash) but if I then use that path for the mris_preproc command I get nsubjects = 22 ERROR: cannot find /scr/etsch2/kids/ct/.long. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:23:48 Betreff: Re: [Freesurfer] cannot find qdec file that is probably not the full path. Try typing ls scr/etsch2/kids/ct/qdec/long.qdec.table.dat If it says it cannot find the file, then it is not the full path. Maybe you need a forward slash (ie, /) in the beginning? On 8/3/15 10:18 AM, Clara Kühn wrote: then I get the error ERROR: cannot find scr/etsch2/kids/ct/qdec/long.qdec.table.dat I had tried that. Sorry, no luck with that. - Ursprüngliche Mail - Von: Douglas Greve gr...@nmr.mgh.harvard.edu An: freesurfer@nmr.mgh.harvard.edu Gesendet: Montag, 3. August 2015 16:16:58 Betreff: Re: [Freesurfer] cannot find qdec file you have to give it the entire path to the file On 8/3/15 10:14 AM, Clara Kühn wrote: Dear FS-experts, I want to analyze my longitudinal data with your suggested LME models and am therefore following the walkthrough by J. Bernal. I get an error though very early on when using the command mris_preproc --qdec-long qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out qdec/lh.thickness.mgh It always says ERROR: cannot find qdec/long.qdec.table.dat Yes, the walkthrough asks for an input file named just qdec.table.dat, but I haven't got that. So far in the longitudinal stream there are long.qdec.table.dat and cross.qdec.table.dat files but no simple qdec.table.dat files. So I figured I'd use the long.qdec file because FS needs to get the information about the long timepoints. But it cannot find the file, even though I see it. I've also tried copying the long.qdec file and naming it qdec.table.dat but it still doesn't find it. The entire path to the file is scr/etsch2/kids/ct/qdec/long.qdec.table.dat and my SUBJECTS_DIR is scr/etsch2/kids/ct Can you help me see what I'm missing? Thanks a lot in advance, Clara ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Weird Freesurfer results
Hi Brent
a quick look and it seems that your answer is yes? You are multiplying
the image intensities by some scale factor?
Bruce
On Tue, 4 Aug 2015, Brent Womble wrote:
Yes. Here is the MATLAB script:
for i = [1:20]
%Load the original image and gray matter mask
raw=load_nii([pwd,'/', num2str(i), '/pre.nii'])
a=single(squeeze(raw.img));
c1_raw=load_nii([pwd,'/', num2str(i), '/c1pre.nii']);
c1=squeeze(c1_raw.img);
%Mask is gray around edges. Threshold to make it binary
c1(c10.1)=1;
%Convert mask to logical
c1=logical(c1);
%%Generate a 3D gaussian kernel
%Specify the origin, size, and intensity of the kernel
k_origin=origins(i,:); %origins is an i by 3 vector to store
all coordinates
k_size=20;
k_intensity=100;
k=1-fspecial3('gaussian',k_size).*k_intensity;
k(k0)=0;
%Expand the kernel to the size of the original image
padsize_pre=k_origin - (k_size/2);
padsize_post=size(a) - k_origin - (k_size/2);
k=padarray(k,padsize_post,1,'post');
k=padarray(k,padsize_pre,1,'pre');
%Restrict the kernel to the gray mask
b=k.*c1;
b(~c1)=1;
%%Apply the kernel to the original image
c=b.*a;
%Write to .nii
raw.img=c;
save_nii(raw,[pwd,'/', num2str(i), '/dense-synth.nii']);
end
On Tue, Aug 4, 2015 at 11:52 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Brent
are you saying you just multiplied the gray matter intensities
by some scale factor (1)?
Bruce
On Tue, 4 Aug 2015, Brent Womble wrote:
Hi everyone,
I've been making synthetic brains to test how
Freesurfer handles various
structural changes.
One of the changes I'm testing is increased density
(like in VBM). To
simulate increased density, I used a spherical
Gaussian multiplication
kernel, with a radius of 20 voxels. I centered this
kernel at a point in
the right superior frontal gyrus and masked the
changes to grey matter using
the segmentation output from SPM12.
Here is an example, a difference image (synth.nii -
pre.nii):
[IMAGE]
Around that area, Freesurfer didn't detect a change
(as I expected):
Inline image 2
Original in red and blue, synthetic in pink and
light blue.
The problem is that the longitudinal streams in
Freesurfer found a bunch of
changes in random parts of the brain.
We looked at the recons for each subject
individually, and saw some noise
around the clusters that were significant in the
two-stage model. This
doesn't make sense, because the actual voxels were
exactly the same in that
region. For example:
[IMAGE]
I redid the recon-all with the -nonormalization
flag. It didn't fix the
problem. For example (same subject as above):
[IMAGE]
I thought it might have been an issue caused by my
increased density method,
so I ran it again, this time with the kernel
centered in the cerebellum
(still masked to grey matter). I still got weird
changes in unrelated parts
of the cortex. For example (same subject as above):
[IMAGE]
Note: light blue/red and blue/red are reversed in
this one, just because of
the order I loaded it in Freeview.
In summary, Freesurfer found a bunch of weird
changes that were nowhere near
the changes I actually made.
Where should I go from here?
-Brent
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Re: [Freesurfer] Weird Freesurfer results
Yes, I'm multiplying the image intensities by a scaling factor. Sorry if
that wasn't clear.
-Brent
On Aug 4, 2015 12:09, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:
Hi Brent
a quick look and it seems that your answer is yes? You are multiplying
the image intensities by some scale factor?
Bruce
On Tue, 4 Aug 2015, Brent Womble wrote:
Yes. Here is the MATLAB script:
for i = [1:20]
%Load the original image and gray matter mask
raw=load_nii([pwd,'/', num2str(i), '/pre.nii'])
a=single(squeeze(raw.img));
c1_raw=load_nii([pwd,'/', num2str(i), '/c1pre.nii']);
c1=squeeze(c1_raw.img);
%Mask is gray around edges. Threshold to make it binary
c1(c10.1)=1;
%Convert mask to logical
c1=logical(c1);
%%Generate a 3D gaussian kernel
%Specify the origin, size, and intensity of the kernel
k_origin=origins(i,:); %origins is an i by 3 vector to store
all coordinates
k_size=20;
k_intensity=100;
k=1-fspecial3('gaussian',k_size).*k_intensity;
k(k0)=0;
%Expand the kernel to the size of the original image
padsize_pre=k_origin - (k_size/2);
padsize_post=size(a) - k_origin - (k_size/2);
k=padarray(k,padsize_post,1,'post');
k=padarray(k,padsize_pre,1,'pre');
%Restrict the kernel to the gray mask
b=k.*c1;
b(~c1)=1;
%%Apply the kernel to the original image
c=b.*a;
%Write to .nii
raw.img=c;
save_nii(raw,[pwd,'/', num2str(i), '/dense-synth.nii']);
end
On Tue, Aug 4, 2015 at 11:52 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
Hi Brent
are you saying you just multiplied the gray matter intensities
by some scale factor (1)?
Bruce
On Tue, 4 Aug 2015, Brent Womble wrote:
Hi everyone,
I've been making synthetic brains to test how
Freesurfer handles various
structural changes.
One of the changes I'm testing is increased density
(like in VBM). To
simulate increased density, I used a spherical
Gaussian multiplication
kernel, with a radius of 20 voxels. I centered this
kernel at a point in
the right superior frontal gyrus and masked the
changes to grey matter using
the segmentation output from SPM12.
Here is an example, a difference image (synth.nii -
pre.nii):
[IMAGE]
Around that area, Freesurfer didn't detect a change
(as I expected):
Inline image 2
Original in red and blue, synthetic in pink and
light blue.
The problem is that the longitudinal streams in
Freesurfer found a bunch of
changes in random parts of the brain.
We looked at the recons for each subject
individually, and saw some noise
around the clusters that were significant in the
two-stage model. This
doesn't make sense, because the actual voxels were
exactly the same in that
region. For example:
[IMAGE]
I redid the recon-all with the -nonormalization
flag. It didn't fix the
problem. For example (same subject as above):
[IMAGE]
I thought it might have been an issue caused by my
increased density method,
so I ran it again, this time with the kernel
centered in the cerebellum
(still masked to grey matter). I still got weird
changes in unrelated parts
of the cortex. For example (same subject as above):
[IMAGE]
Note: light blue/red and blue/red are reversed in
this one, just because of
the order I loaded it in Freeview.
In summary, Freesurfer found a bunch of weird
changes that were nowhere near
the changes I actually made.
Where should I go from here?
-Brent
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[Freesurfer] bbregister --12?
Hi all, I am using a previous script to update a pipeline for pre-processing diffusion data. My objective related to this question is the (what I think is a hidden) argument “- -12” when using bbregister (v. 1.49.2.3 FreeSurfer 5.3). Will this denote 12 degrees of freedom for my registration? If so, why is this argument hidden (not in the manual or --help) and what are your insights when registering diffusion data to the Freesurfer T1 image? Should I keep 12dof or just do a simple rigid body registraion (e.g. 6 dof) Thanks in advance for your response, Rodrigo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] qdec - Generate stats data table
You can just run recon-all with the -wmparc flag. It should be pretty quick, less than 30 min or soo On 08/04/2015 12:04 PM, pablo najt wrote: Thank you this subject had a zip copy of the wmparc.stats Now I am missing this file from another subject. Do I need to run recon-all from start or is there a shortcut for getting this file? Thanks Doug. Pablo Date: Tue, 4 Aug 2015 11:42:43 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec - Generate stats data table Have you looked in /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats to see if there might be a problem? On 08/04/2015 05:43 AM, pablo najt wrote: Dear FS experts, I am trying to generate my stats data tables with QDEC -after successfully loading my data table- and come across the following error. Any recommendations would be greatly appreciated. Thank you in advance Pablo Data table loading completed successfully. SUBJECTS_DIR is '/Volumes/NEW_VOLUME/GBS' mkdir -p /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/ -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files Building the table.. Writing the table to /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/wmparc.volume.stats.dat --statsfile=wmparc.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files ERROR: The stats file /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files ___ 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
Re: [Freesurfer] A problem in publication (citation with freesurfer))
You don't need to cite mri_label2vol, it is just a spatial transformation On 08/02/2015 09:21 PM, jinyi wrote: Hello freesurfers I am working on a paper based on freesurfer and other images process tools. I am wondering the citation problems, In the freesurfer wiki, a help page (http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFiledo=viewtarget=freesurfer_methods.doc) is about it. But it is too short for me. On this page, The reconstrction technique details are from many papers. So should I cite them all? And I mainly use recon-all to reconstruction the brain and mri_label2vol to extract some parts from the 3D brain in my work, but the Wiki do not provide the papers about mri_label2vol. What papers should I cite? Wating for your response. With personal regards. ___ 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] randomness and aseg stats
We ran freesurfer on a participant with randomness flag enabled on a separate OS (centOS vs. unbuntu) and we still get the exact same aseg.stats values. Our question is does the randomness flag vary the results in aseg.stats like it does with aparc.stats Prashanth Nyalakanti pnyalaka...@mrn.org ___ 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] contrasts
The F would be 1 -1 0 0 0 0 -1 0 Your t-contrasts are correct (you don't need to do both directions) On 08/03/2015 03:40 PM, Lim, Lena wrote: Hi experts, I have 3 groups: (A, PC and HC) and 1 covariate: IQ. For a DOSS file, how should I define the F contrast? Would it still be: I -1 0 ? 1 0 -1 And would the t contrast for say APC be: 1 -1 0 0 and for A PC be -1 1 0 0 etc Many thanks, Lena ___ 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] Dimension mismatch between mask and run
There is still a warning about multiple formats. This means you have not deleted all the offending files. On 08/04/2015 12:19 PM, Rodriguez-Thompson, Anais wrote: Hi Doug, Thanks for getting back to me. I tried deleting those files, and got the same error, although the terminal output looked slightly different towards the end (in terms of the compensation values). Here it is below: -- selxavg3-sess logfile is /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_050514-150804121216.log -- preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_050514 -nolog -- preproc-sess logfile is /dev/null -- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ arodthom setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_050514 -nolog Tue Aug 4 12:12:17 EDT 2015 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 fmcpr mask 1 brain GDDA098 Template - mktemplate-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile -nolog -update Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Tue Aug 4 12:12:17 EDT 2015 Detected input format at nii GDDA098 Update not needed Run: 015 Tue Aug 4 12:12:17 EDT 2015 GDDA098 015 Update not needed Run: 016 Tue Aug 4 12:12:17 EDT 2015 GDDA098 016 Update not needed Run: 017 Tue Aug 4 12:12:17 EDT 2015 GDDA098 017 Update not needed Tue Aug 4 12:12:17 EDT 2015 mktemplate-sess completed GDDA098 Mask mkbrainmask-sess -maskstem brain -fsd bold -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Tue Aug 4 12:12:17 EDT 2015 WARNING: multiple formats found for template USING: template.nii.gz GDDA098 Update not needed for session-level mask WARNING: multiple formats found for 015/template USING: 015/template.nii.gz GDDA098 Update not needed for run 015 mask GDDA098 Update not needed for run 015 meanval WARNING: multiple formats found for 016/template USING: 016/template.nii.gz GDDA098 Update not needed for run 016 mask GDDA098 Update not needed for run 016 meanval WARNING: multiple formats found for 017/template USING: 017/template.nii.gz GDDA098 Update not needed for run 017 mask GDDA098 Update not needed for run 017 meanval Tue Aug 4 12:12:18 EDT 2015 mkbrainmask-sess done GDDA098 Registration - register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update -- register-sess logfile is /dev/null -- Tue Aug 4 12:12:18 EDT 2015 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Tue Aug 4 12:12:18 EDT 2015 Run: 015 Tue Aug 4 12:12:18 EDT 2015 WARNING: multiple formats found for bold/015/template USING: bold/015/template.nii.gz Update not needed Run: 016 Tue Aug 4 12:12:18 EDT 2015 WARNING: multiple formats found for bold/016/template USING: bold/016/template.nii.gz Update not needed Run: 017 Tue Aug 4 12:12:18 EDT 2015 WARNING: multiple formats found for bold/017/template USING: bold/017/template.nii.gz Update not needed Tue Aug 4 12:12:18 EDT 2015 register-sess completed GDDA098 MC - mc-sess -fstem f -fmcstem fmcpr -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile -per-run -nolog
Re: [Freesurfer] bbregister --12?
Great, thank you for your help! On 8/4/15, 2:36 PM, freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N Greve freesurfer-boun...@nmr.mgh.harvard.edu on behalf of gr...@nmr.mgh.harvard.edu wrote: Yes, it is for 12dof. It is not hidden for any particular purpose (except maybe that I'm lazy). In general, I don't think it is a good idea to use 12 or 9 dof unless you have an explicit reason to. On 08/04/2015 01:54 PM, Perea Camargo, Rodrigo Dennis wrote: Hi all, I am using a previous script to update a pipeline for pre-processing diffusion data. My objective related to this question is the (what I think is a hidden) argument ³- -12² when using bbregister (v. 1.49.2.3 FreeSurfer 5.3). Will this denote 12 degrees of freedom for my registration? If so, why is this argument hidden (not in the manual or --help) and what are your insights when registering diffusion data to the Freesurfer T1 image? Should I keep 12dof or just do a simple rigid body registraion (e.g. 6 dof) Thanks in advance for your response, Rodrigo ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] recon-all exited with errors
Thank you, Zeke for your help! Best wishes, Hisako -Original Message- From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] Sent: Tuesday, August 04, 2015 4:08 PM To: Freesurfer support list; Fujiwara, Hisako Subject: Re: [Freesurfer] recon-all exited with errors Hello Hisako, This is a recently discovered bug either mni related or VirtualBox related. The issue is that the mri_nu_correct.mni command will fail when executed in the VirtualBox environment on a subject whose data exists on a shared folder between the host and the virtual machine. Currently, the only known solution is to import the subject data folder into the VirtualBox environment, and then run recon-all. -Zeke On 08/04/2015 11:19 AM, Fujiwara, Hisako wrote: Hello, I am very new to freesurfer who have been using SPM and FSL, and just started doing individual subject analysis. I already had an error message on recon-all step. I am using: Vertualbox, OS is RedHat 64-bit I am using bash (I prefer to do so) so I am not in tsch shell. The recon-all process was terminated with error but not sure exactly what the error was even I looked at the recon-all.log file which is attached to this e-mail. According to the line of script, there should be a file called 'talairach.xfm in /mri/transforms folder but I see only the folder called 'bak' which is empty. Please advise what is the exact error is and how to solve this problem. Thank you so much for your help in advance. Hisako * fsuser@xubuntu-VirtualBox:/media/sf_shared_folder/CAE_MRI$ recon-all -i CAE_2_1_T1.nii -subject CAE_2_1 -all WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /media/sf_shared_folder Actual FREESURFER_HOME /usr/local/freesurfer Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux /media/sf_shared_folder/CAE_2_1 mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz... # #@# MotionCor Tue Aug 4 10:04:50 EDT 2015 Found 1 runs /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz /media/sf_shared_folder/CAE_2_1 mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) Original Data has (0.976562, 0.976562, 1) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /media/sf_shared_folder/CAE_2_1/mri/orig.mgz... mri_add_xform_to_header -c /media/sf_shared_folder/CAE_2_1/mri/transforms/talairach.xfm /media/sf_shared_folder/CAE_2_1/mri/orig.mgz /media/sf_shared_folder/CAE_2_1/mri/orig.mgz INFO: extension is mgz # #@# Talairach Tue Aug 4 10:05:06 EDT 2015 /media/sf_shared_folder/CAE_2_1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux recon-all -s CAE_2_1 exited with ERRORS at Tue Aug 4 10:05:13 EDT 2015 For more details, see the log file /media/sf_shared_folder/CAE_2_1/scripts/recon-all.log To report a problem, see https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.har vard.edu_fswiki_BugReportingd=BQIF-gc=P0c35rBvlN7D8BNx7kSJTgr=irT_w sJtD80udNn2jMvx1MUsr-k7TAFC5R4iJrY-rOAm=CNRhBZT-7el4JHrXWT1pMkcCxTr7n AiwdW0KqdCmL-0s=77s99nYShDEQhOUBas6lQvd60QUPBdrcqJYMzY93ExMe=
[Freesurfer] Using FSL commands through Matlab (Linux)
Hello,
Sorry if this isn’t the right forum for the question, but not sure where to
direct it.
I’m trying to incorporate some FSL commands into a Matlab script. I’m using a
Linux machine and running Matlab 7.11.0 (2010b). I tried to access the FSL
toolbox through Matlab using:
setenv(‘FSLDIR’,’/autofs/cluster/pubsw/2/pubsw/Linux-2-2.3-x86_64/packages/fsl.64bit/5.0.7’)
system(‘${FSLDIR}/etc/fslconf/fsl.sh’)
But received a “permissions denied” error. Is there an easier way to access FSL
through Matlab?
Thanks,
Daniel S. Albrecht, PhD
Research Fellow in Radiology
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-6748
Fax: (617) 726-7422
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Re: [Freesurfer] Using FSL commands through Matlab (Linux)
Ah, that's probably correct. I think it worked on my system because I source
the FSL conf file in my .bashrc
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Tuesday, August 04, 2015 4:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Using FSL commands through Matlab (Linux)
I don't think that will work because the shell where FSLDIR gets set is
not the same shell as that of the system command. Try putting those two
in the same string and then running system on that
On 08/04/2015 04:36 PM, Albrecht, Daniel S. wrote:
Hello,
Sorry if this isn’t the right forum for the question, but not sure
where to direct it.
I’m trying to incorporate some FSL commands into a Matlab script. I’m
using a Linux machine and running Matlab 7.11.0 (2010b). I tried to
access the FSL toolbox through Matlab using:
setenv(‘FSLDIR’,’/autofs/cluster/pubsw/2/pubsw/Linux-2-2.3-x86_64/packages/fsl.64bit/5.0.7’)
system(‘${FSLDIR}/etc/fslconf/fsl.sh’)
But received a “permissions denied” error. Is there an easier way to
access FSL through Matlab?
Thanks,
Daniel S. Albrecht, PhD
Research Fellow in Radiology
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-6748
Fax: (617) 726-7422
dsalbre...@mgh.harvard.edu
https://urldefense.proofpoint.com/v2/url?u=https-3A__owa.partners.org_cvpn_aHR0cHM6Ly9wcm94eS1vd2EucGFydG5lcnMub3Jn_owa_redir.aspx-3FC-3D8A9OJCUaPkOLxUmmjc0-5FcF-2DxdjAP2NEI4aEbq2JpVjitXhs-5FQYjcIRXVbcEtTXWjym0XzqsaDNI.-26URL-3Dmailto-253amarco-2540nmr.mgh.harvard.edud=BQIF-gc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5jbDc-vHb9P3-hkq5C4m=MIxMSVH7VHFSDpQ8-QJrLgfoMt9e6HC2psPqEbMEK6Is=Rw2JY9Xtl--NIzjOAN4aCfl_jzhxYbB2ek1lDWBLJAge=
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop:
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Outgoing:
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Re: [Freesurfer] Error while using mri_glmfit
Not sure. I guess you could say the duration is 0 for the controls, but it has to make sense for your data, which I cannot tell you On 08/04/2015 04:29 PM, Matthieu Vanhoutte wrote: Thanks for quick answer ! How could I regress out the effect of epilepsy duration on patients, knowing that this factor is null for controls ? Cheers, Matthieu Le 4 août 2015 22:22, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu a écrit : The Epilepsy_Duration is the same for all MaleControl subjects. You can't use that as a covariate if it does not have any variation On 08/04/2015 04:10 PM, Matthieu Vanhoutte wrote: Douglas, Please fond attached the fsgd file. Cheers, Matthieu Le 4 août 2015 21:45, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu a écrit : can you send the fsgd file? On 08/04/2015 03:42 PM, Matthieu Vanhoutte wrote: Hello experts, Could anyone provide me an advice or answer to this problem ? Thanks in advance ! Best regards, Matthieu Le 28 juil. 2015 14:12, Matthieu Vanhoutte matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com a écrit : Dear Freesurfer's Experts, Please find below an error occuring when I use mri_glmfit : Design matrix -- 1.000 0.000 0.000 0.000 0.000 0.000 9.804 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -10.612 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -21.114 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -12.936 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 15.129 0.000 0.000 0.000 0.000 0.000 17.562 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 16.402 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -6.889 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 10.584 0.000 0.000 0.000 0.000 0.000 37.017 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.243 0.000 0.000 0.000 0.000 0.000 7.675 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 20.432 0.000 0.000 0.000 0.000 0.000 43.865 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.287 0.000 0.000 0.000 0.000 0.000 23.719 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 10.735 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.734 0.000 0.000 0.000 0.000 0.000 21.167 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -8.197 0.000 0.000 0.000 0.000 0.000 -2.765 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -3.431 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -18.456 0.000 0.000 0.000 0.000 0.000 4.976; 1.000 0.000 0.000 0.000 0.000 0.000 -18.437 0.000 0.000 0.000 0.000
Re: [Freesurfer] Regarding different sample size
The statistics will work properly, but they do assume that the variances are the same in different groups. This assumption is generally ok if you have a balanced design, which you don't. Also, your p-values are going to be driven by the lowest number of subjects. With only 5 you might not see much of an effect On 07/30/2015 01:53 PM, Dibashree Tamuli wrote: Dear Freesufer Experts, I would like to ask about any tool of freesurfer for comparing cortical thickness of different sample size. Let me describe: I have 3 groups of different sample size (n=25, n=15, n=5) and control (n=8). Is it possible to compare ? Thanks and regards Dibashree AIIMS, New Delhi ___ 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] Dimension mismatch between mask and run
sorry, I don't remember what that thread is. Can you repost with the thread in the email? On 08/04/2015 03:20 PM, Rodriguez-Thompson, Anais wrote: Hi Doug, I deleted all of the template.nii files, and now the command works. Thank you for your advice! In regards to my other thread (selxavg3-sess error), where selxavg3 looks for a file that doesn't exist (fmcpr.sm5.nii.gz), could I rename the preproc-sess output volume (fmcpr.nii.gz) to fmcpr.sm5.nii.gz in order to run the command? Given preproc-sess at -fwhm 5, this volume should be smoothed at 5 and should be the input for analysis, correct? Thanks, Anais 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, August 04, 2015 3:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Dimension mismatch between mask and run There is still a warning about multiple formats. This means you have not deleted all the offending files. On 08/04/2015 12:19 PM, Rodriguez-Thompson, Anais wrote: Hi Doug, Thanks for getting back to me. I tried deleting those files, and got the same error, although the terminal output looked slightly different towards the end (in terms of the compensation values). Here it is below: -- selxavg3-sess logfile is /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_050514-150804121216.log -- preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_050514 -nolog -- preproc-sess logfile is /dev/null -- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ arodthom setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_050514 -nolog Tue Aug 4 12:12:17 EDT 2015 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 fmcpr mask 1 brain GDDA098 Template - mktemplate-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile -nolog -update Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Tue Aug 4 12:12:17 EDT 2015 Detected input format at nii GDDA098 Update not needed Run: 015 Tue Aug 4 12:12:17 EDT 2015 GDDA098 015 Update not needed Run: 016 Tue Aug 4 12:12:17 EDT 2015 GDDA098 016 Update not needed Run: 017 Tue Aug 4 12:12:17 EDT 2015 GDDA098 017 Update not needed Tue Aug 4 12:12:17 EDT 2015 mktemplate-sess completed GDDA098 Mask mkbrainmask-sess -maskstem brain -fsd bold -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Tue Aug 4 12:12:17 EDT 2015 WARNING: multiple formats found for template USING: template.nii.gz GDDA098 Update not needed for session-level mask WARNING: multiple formats found for 015/template USING: 015/template.nii.gz GDDA098 Update not needed for run 015 mask GDDA098 Update not needed for run 015 meanval WARNING: multiple formats found for 016/template USING: 016/template.nii.gz GDDA098 Update not needed for run 016 mask GDDA098 Update not needed for run 016 meanval WARNING: multiple formats found for 017/template USING: 017/template.nii.gz GDDA098 Update not needed for run 017 mask GDDA098 Update not needed for run 017 meanval Tue Aug 4 12:12:18 EDT 2015 mkbrainmask-sess done GDDA098 Registration - register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update -- register-sess logfile is /dev/null -- Tue Aug 4 12:12:18 EDT 2015 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or
Re: [Freesurfer] recon-all -s FrSrfr_Recon exited with ERRORS
Hello, This is a recently discovered bug either mni related or virtual box related. The issue is that the mri_nu_correct.mni command will fail when executed in the VirtualBox environment on a subject whose data exists on a shared folder between the host and the virtual machine. Currently the only known solution is to import the subject data folder into the VirtualBox environment, and then run recon-all. -Zeke On 08/03/2015 11:54 PM, Li, Zhihao wrote: Hi FS experts, I was trying to run recon-all within the VirtualBox of NeuroDebian 8.0 on a WIN8 host. The program stopped immaturely at the step of mri_nu_correct.mni. I went into the folder of mri and ran mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz with the output pasted below. Could you please help me to fix this problem? Thank you very much! --- brain:mri$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux Mon Aug 3 22:51:33 EDT 2015 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.31236 /media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31236/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31236/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.31236/nu0.mnc... Iteration 1 Mon Aug 3 22:51:38 EDT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.31236/nu0.mnc ./tmp.mri_nu_correct.mni.31236/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.31236/0/ -iterations 1000 -distance 50 defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [brain@neurodebian:/media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/mri/] [2015-08-03 22:51:38] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.31236/0/ ./tmp.mri_nu_correct.mni.31236/nu0.mnc ./tmp.mri_nu_correct.mni.31236/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination
Re: [Freesurfer] Error while using mri_glmfit
Thanks for quick answer ! How could I regress out the effect of epilepsy duration on patients, knowing that this factor is null for controls ? Cheers, Matthieu Le 4 août 2015 22:22, Douglas N Greve gr...@nmr.mgh.harvard.edu a écrit : The Epilepsy_Duration is the same for all MaleControl subjects. You can't use that as a covariate if it does not have any variation On 08/04/2015 04:10 PM, Matthieu Vanhoutte wrote: Douglas, Please fond attached the fsgd file. Cheers, Matthieu Le 4 août 2015 21:45, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu a écrit : can you send the fsgd file? On 08/04/2015 03:42 PM, Matthieu Vanhoutte wrote: Hello experts, Could anyone provide me an advice or answer to this problem ? Thanks in advance ! Best regards, Matthieu Le 28 juil. 2015 14:12, Matthieu Vanhoutte matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com a écrit : Dear Freesurfer's Experts, Please find below an error occuring when I use mri_glmfit : Design matrix -- 1.000 0.000 0.000 0.000 0.000 0.000 9.804 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -10.612 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -21.114 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -12.936 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 15.129 0.000 0.000 0.000 0.000 0.000 17.562 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 16.402 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -6.889 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 10.584 0.000 0.000 0.000 0.000 0.000 37.017 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.243 0.000 0.000 0.000 0.000 0.000 7.675 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 20.432 0.000 0.000 0.000 0.000 0.000 43.865 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.287 0.000 0.000 0.000 0.000 0.000 23.719 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 10.735 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.734 0.000 0.000 0.000 0.000 0.000 21.167 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -8.197 0.000 0.000 0.000 0.000 0.000 -2.765 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -3.431 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -18.456 0.000 0.000 0.000 0.000 0.000 4.976; 1.000 0.000 0.000 0.000 0.000 0.000 -18.437 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.150 0.000 0.000 0.000 0.000 0.000 -1.417 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -16.936 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -3.442 0.000 0.000 0.000 0.000 0.000 21.991 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 9.298 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 6.360 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000
Re: [Freesurfer] Using FSL commands through Matlab (Linux)
I don't think that will work because the shell where FSLDIR gets set is
not the same shell as that of the system command. Try putting those two
in the same string and then running system on that
On 08/04/2015 04:36 PM, Albrecht, Daniel S. wrote:
Hello,
Sorry if this isn’t the right forum for the question, but not sure
where to direct it.
I’m trying to incorporate some FSL commands into a Matlab script. I’m
using a Linux machine and running Matlab 7.11.0 (2010b). I tried to
access the FSL toolbox through Matlab using:
setenv(‘FSLDIR’,’/autofs/cluster/pubsw/2/pubsw/Linux-2-2.3-x86_64/packages/fsl.64bit/5.0.7’)
system(‘${FSLDIR}/etc/fslconf/fsl.sh’)
But received a “permissions denied” error. Is there an easier way to
access FSL through Matlab?
Thanks,
Daniel S. Albrecht, PhD
Research Fellow in Radiology
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-6748
Fax: (617) 726-7422
dsalbre...@mgh.harvard.edu
https://owa.partners.org/cvpn/aHR0cHM6Ly9wcm94eS1vd2EucGFydG5lcnMub3Jn/owa/redir.aspx?C=8A9OJCUaPkOLxUmmjc0_cF-xdjAP2NEI4aEbq2JpVjitXhs_QYjcIRXVbcEtTXWjym0XzqsaDNI.URL=mailto%3amarco%40nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] selxavg3-sess error
Sorry, disregard my previous email! I just realized that I should have created a new message thread. Below is the previous email thread. Given this issue, could I rename the preproc-sess output volume (fmcpr.nii.gz) to fmcpr.sm5.nii.gz in order to run the command? Given preproc-sess at -fwhm 5, this volume should be smoothed at 5 and should be the input for analysis, correct? Thanks, Anais 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: Thursday, July 30, 2015 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error ok, still not sure what is happening. Can you try preproc-sess -debug -s GDDA001 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_072915 | tee doug2.log and send me doug2.log On 07/30/2015 12:54 PM, Rodriguez-Thompson, Anais wrote: Hi Doug, Below are the contents of doug.log: set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return foreach grp ( $grpdefs ) foreach grp ( ) goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#SearchPathList == 0 ) then if ( 0 == 0 ) then set SearchPathList = . ; set SearchPathList = . endif endif goto check_params_return ; goto check_params_return set UniqueList = ( ) ; set UniqueList = ( ) foreach d ( $SearchPathList ) foreach d ( . ) if ( ! -e $d ) then if ( ! -e . ) then set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ; if ( 1 ) set UniqueList = ( . ) set UniqueList = ( . ) end end set SearchPathList = ( $UniqueList ) ; set SearchPathList = ( . ) set errs = 0 ; set errs = 0 set SessPath = ( ) ; set SessPath = ( ) foreach sess ( $SessList ) foreach sess ( GDDA001 ) set tmp = ( ) ; set tmp = ( ) foreach d ( $SearchPathList ) foreach d ( . ) set stst = $d/$sess set stst = ./GDDA001 if ( -d $stst ) then if ( -d ./GDDA001 ) then if ( ! -r $stst ) then if ( ! -r ./GDDA001 ) then pushd $stst /dev/null ; pushd ./GDDA001 set tmp = ( $tmp `$PWDCMD` ) ; set tmp = ( `$PWDCMD` ) pwd popd /dev/null ; popd endif endif end end set nfound = ( $#tmp ) ; set nfound = ( 1 ) if ( $nfound == 0 ) then if ( 1 == 0 ) then if ( $nfound 1 ) then if ( 1 1 ) then set SessPath = ( $SessPath $tmp ) ; set SessPath = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) end end set UniqueList = ( ) ; set UniqueList = ( ) foreach s ( $SessPath ) foreach s ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( ! $IsUnique ! $AllowRedundant ) then if ( ! 1 ! 0 ) then set UniqueList = ( $UniqueList $s ) ; set UniqueList = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) endif endif end end echo $SessPath echo /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 exit $errs ; exit 0 set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#analysis == 0 $flacfile == 0 ) then if ( 1 == 0 == 0 ) then if ( $#analysis != 0 ) then if ( 1 != 0 ) then if ( ! -d $analysis ) then if ( ! -d SIRP_LoadRegression_Stable5_072915 ) then if ( ! -e $analysis/analysis.info ) then if ( ! -e SIRP_LoadRegression_Stable5_072915/analysis.info ) then endif endif if ( $#flacfile != 0 ) then if ( 0 != 0 ) then if ( $perrun $jkrun ) then if ( 0 0 ) then if ( $UseOctave ) then if ( 0 ) then goto check_params_return ; goto check_params_return set StudyDir = `pwd` ; set StudyDir = `pwd` pwd if ( $#analysis ) then if ( 1 ) then set analysisname = $analysis set analysisname = SIRP_LoadRegression_Stable5_072915 set fsd = `getana -a $analysis -t fsd` ; set fsd = `getana -a $analysis -t fsd` getana -a SIRP_LoadRegression_Stable5_072915 -t fsd set PerSession = `getana -a $analysis -t IsPerSession` set PerSession = `getana -a $analysis -t IsPerSession` getana -a SIRP_LoadRegression_Stable5_072915 -t IsPerSession set IsNative = `getana -a $analysis -t IsNative` set IsNative = `getana -a $analysis -t IsNative` getana -a SIRP_LoadRegression_Stable5_072915 -t IsNative set IsSurface = `getana -a $analysis -t IsSurface` set IsSurface = `getana -a $analysis -t IsSurface` getana -a SIRP_LoadRegression_Stable5_072915 -t IsSurface if ( $IsSurface ) then if ( 0 ) then set dt = `getana -a $analysis -t designtype` set dt = `getana -a $analysis -t designtype` getana -a SIRP_LoadRegression_Stable5_072915 -t designtype if ( $dt == abblocked ) set RequireContrasts = 0 ; if ( event-related == abblocked ) set RequireContrasts = 0 if ( $dt ==
Re: [Freesurfer] recon-all exited with errors
Hello Hisako, This is a recently discovered bug either mni related or VirtualBox related. The issue is that the mri_nu_correct.mni command will fail when executed in the VirtualBox environment on a subject whose data exists on a shared folder between the host and the virtual machine. Currently, the only known solution is to import the subject data folder into the VirtualBox environment, and then run recon-all. -Zeke On 08/04/2015 11:19 AM, Fujiwara, Hisako wrote: Hello, I am very new to freesurfer who have been using SPM and FSL, and just started doing individual subject analysis. I already had an error message on recon-all step. I am using: Vertualbox, OS is RedHat 64-bit I am using bash (I prefer to do so) so I am not in tsch shell. The recon-all process was terminated with error but not sure exactly what the error was even I looked at the recon-all.log file which is attached to this e-mail. According to the line of script, there should be a file called ‘talairach.xfm in /mri/transforms folder but I see only the folder called ‘bak’ which is empty. Please advise what is the exact error is and how to solve this problem. Thank you so much for your help in advance. Hisako * fsuser@xubuntu-VirtualBox:/media/sf_shared_folder/CAE_MRI$ recon-all -i CAE_2_1_T1.nii -subject CAE_2_1 -all WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /media/sf_shared_folder Actual FREESURFER_HOME /usr/local/freesurfer Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux /media/sf_shared_folder/CAE_2_1 mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz mri_convert /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/sf_shared_folder/CAE_MRI/CAE_2_1_T1.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) writing to /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz... # #@# MotionCor Tue Aug 4 10:04:50 EDT 2015 Found 1 runs /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /media/sf_shared_folder/CAE_2_1/mri/orig/001.mgz /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz /media/sf_shared_folder/CAE_2_1 mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform mri_convert /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz /media/sf_shared_folder/CAE_2_1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /media/sf_shared_folder/CAE_2_1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, 0, 0) Original Data has (0.976562, 0.976562, 1) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /media/sf_shared_folder/CAE_2_1/mri/orig.mgz... mri_add_xform_to_header -c /media/sf_shared_folder/CAE_2_1/mri/transforms/talairach.xfm /media/sf_shared_folder/CAE_2_1/mri/orig.mgz /media/sf_shared_folder/CAE_2_1/mri/orig.mgz INFO: extension is mgz # #@# Talairach Tue Aug 4 10:05:06 EDT 2015 /media/sf_shared_folder/CAE_2_1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux xubuntu-VirtualBox 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:41:14 UTC 2012 i686 i686 i386 GNU/Linux recon-all -s CAE_2_1 exited with ERRORS at Tue Aug 4 10:05:13 EDT 2015 For more details, see the log file /media/sf_shared_folder/CAE_2_1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting fsuser@xubuntu-VirtualBox:/media/sf_shared_folder/CAE_MRI$ ___ 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
Re: [Freesurfer] Using FSL commands through Matlab (Linux)
Just use either system or the exclamation mark and type the FSL commands
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Albrecht, Daniel S.
[dsalbre...@mgh.harvard.edu]
Sent: Tuesday, August 04, 2015 4:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Using FSL commands through Matlab (Linux)
Hello,
Sorry if this isn’t the right forum for the question, but not sure where to
direct it.
I’m trying to incorporate some FSL commands into a Matlab script. I’m using a
Linux machine and running Matlab 7.11.0 (2010b). I tried to access the FSL
toolbox through Matlab using:
setenv(‘FSLDIR’,’/autofs/cluster/pubsw/2/pubsw/Linux-2-2.3-x86_64/packages/fsl.64bit/5.0.7’)
system(‘${FSLDIR}/etc/fslconf/fsl.sh’)
But received a “permissions denied” error. Is there an easier way to access FSL
through Matlab?
Thanks,
Daniel S. Albrecht, PhD
Research Fellow in Radiology
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-6748
Fax: (617) 726-7422
dsalbre...@mgh.harvard.eduhttps://urldefense.proofpoint.com/v2/url?u=https-3A__owa.partners.org_cvpn_aHR0cHM6Ly9wcm94eS1vd2EucGFydG5lcnMub3Jn_owa_redir.aspx-3FC-3D8A9OJCUaPkOLxUmmjc0-5FcF-2DxdjAP2NEI4aEbq2JpVjitXhs-5FQYjcIRXVbcEtTXWjym0XzqsaDNI.-26URL-3Dmailto-253amarco-2540nmr.mgh.harvard.edud=BQMF-gc=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFUr=bw42CATdUgaQuKlfBniyB_kCJBdQgH3uC9uSwd5UzJ12A5jbDc-vHb9P3-hkq5C4m=yoHn5AdM00amaVhhUDcIsepTng10PQv74avERFjQOjYs=AZluQUJkTWvBcj436QwnI3ZFMSgR88-C7ONrBVTUuBQe=
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Re: [Freesurfer] recon-all -s FrSrfr_Recon exited with ERRORS
Hello, What is the contents of the $FREESURFER_HOME/build-stamp.txt file? -Zele On 08/03/2015 11:54 PM, Li, Zhihao wrote: Hi FS experts, I was trying to run recon-all within the VirtualBox of NeuroDebian 8.0 on a WIN8 host. The program stopped immaturely at the step of mri_nu_correct.mni. I went into the folder of mri and ran mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz with the output pasted below. Could you please help me to fix this problem? Thank you very much! --- brain:mri$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux Mon Aug 3 22:51:33 EDT 2015 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.31236 /media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31236/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.31236/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2530.00, TE=3.45, TI=1100.00, flip angle=7.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.31236/nu0.mnc... Iteration 1 Mon Aug 3 22:51:38 EDT 2015 nu_correct -clobber ./tmp.mri_nu_correct.mni.31236/nu0.mnc ./tmp.mri_nu_correct.mni.31236/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.31236/0/ -iterations 1000 -distance 50 defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [brain@neurodebian:/media/sf_host/SZU_ZL_3WAY/test/T1/FrSrfr_Recon/mri/] [2015-08-03 22:51:38] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.31236/0/ ./tmp.mri_nu_correct.mni.31236/nu0.mnc ./tmp.mri_nu_correct.mni.31236/nu1.imp Assertion failed at line 827 in file templates/CachedArray.cc nu_estimate_np_and_em: crashed while running volume_stats (termination status=256) nu_correct: crashed while running nu_estimate_np_and_em (termination status=256) ERROR: nu_correct ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer
Re: [Freesurfer] Dimension mismatch between mask and run
Hi Doug, Below this email is the email thread. I was wondering whether I could rename the preproc-sess output volume (fmcpr.nii.gz) to fmcpr.sm5.nii.gz in order to run the command. Given preproc-sess at -fwhm 5, this volume should be smoothed at 5 and should be the input for analysis, correct? Thanks, Anais From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Rodriguez-Thompson, Anais [arodriguez-thomp...@mgh.harvard.edu] Sent: Thursday, July 30, 2015 6:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] selxavg3-sess error Hi Doug, Attached is doug2.log. Thanks, Anais 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: Thursday, July 30, 2015 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] selxavg3-sess error ok, still not sure what is happening. Can you try preproc-sess -debug -s GDDA001 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_072915 | tee doug2.log and send me doug2.log On 07/30/2015 12:54 PM, Rodriguez-Thompson, Anais wrote: Hi Doug, Below are the contents of doug.log: set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return foreach grp ( $grpdefs ) foreach grp ( ) goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#SearchPathList == 0 ) then if ( 0 == 0 ) then set SearchPathList = . ; set SearchPathList = . endif endif goto check_params_return ; goto check_params_return set UniqueList = ( ) ; set UniqueList = ( ) foreach d ( $SearchPathList ) foreach d ( . ) if ( ! -e $d ) then if ( ! -e . ) then set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( $IsUnique ) set UniqueList = ( $UniqueList $d ) ; if ( 1 ) set UniqueList = ( . ) set UniqueList = ( . ) end end set SearchPathList = ( $UniqueList ) ; set SearchPathList = ( . ) set errs = 0 ; set errs = 0 set SessPath = ( ) ; set SessPath = ( ) foreach sess ( $SessList ) foreach sess ( GDDA001 ) set tmp = ( ) ; set tmp = ( ) foreach d ( $SearchPathList ) foreach d ( . ) set stst = $d/$sess set stst = ./GDDA001 if ( -d $stst ) then if ( -d ./GDDA001 ) then if ( ! -r $stst ) then if ( ! -r ./GDDA001 ) then pushd $stst /dev/null ; pushd ./GDDA001 set tmp = ( $tmp `$PWDCMD` ) ; set tmp = ( `$PWDCMD` ) pwd popd /dev/null ; popd endif endif end end set nfound = ( $#tmp ) ; set nfound = ( 1 ) if ( $nfound == 0 ) then if ( 1 == 0 ) then if ( $nfound 1 ) then if ( 1 1 ) then set SessPath = ( $SessPath $tmp ) ; set SessPath = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) end end set UniqueList = ( ) ; set UniqueList = ( ) foreach s ( $SessPath ) foreach s ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) set IsUnique = 1 ; set IsUnique = 1 foreach u ( $UniqueList ) foreach u ( ) if ( ! $IsUnique ! $AllowRedundant ) then if ( ! 1 ! 0 ) then set UniqueList = ( $UniqueList $s ) ; set UniqueList = ( /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 ) endif endif end end echo $SessPath echo /autofs/cluster/roffman/users/Stable5_PerRun/GDDA001 exit $errs ; exit 0 set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 0 != 0 ) goto parse_args_return ; goto parse_args_return goto check_params ; goto check_params if ( $#SessList == 0 ) then if ( 1 == 0 ) then if ( $#analysis == 0 $flacfile == 0 ) then if ( 1 == 0 == 0 ) then if ( $#analysis != 0 ) then if ( 1 != 0 ) then if ( ! -d $analysis ) then if ( ! -d SIRP_LoadRegression_Stable5_072915 ) then if ( ! -e $analysis/analysis.info ) then if ( ! -e SIRP_LoadRegression_Stable5_072915/analysis.info ) then endif endif if ( $#flacfile != 0 ) then if ( 0 != 0 ) then if ( $perrun $jkrun ) then if ( 0 0 ) then if ( $UseOctave ) then if ( 0 ) then goto check_params_return ; goto check_params_return set StudyDir = `pwd` ; set StudyDir = `pwd` pwd if ( $#analysis ) then if ( 1 ) then set analysisname = $analysis set analysisname = SIRP_LoadRegression_Stable5_072915 set fsd = `getana -a $analysis -t fsd` ; set fsd = `getana -a $analysis -t fsd` getana -a SIRP_LoadRegression_Stable5_072915 -t fsd set PerSession = `getana -a $analysis -t IsPerSession` set PerSession = `getana -a $analysis -t IsPerSession` getana -a SIRP_LoadRegression_Stable5_072915 -t IsPerSession set IsNative = `getana -a $analysis -t IsNative` set IsNative = `getana -a $analysis -t IsNative` getana -a SIRP_LoadRegression_Stable5_072915 -t IsNative set IsSurface = `getana -a $analysis -t IsSurface` set IsSurface = `getana -a $analysis -t IsSurface` getana -a SIRP_LoadRegression_Stable5_072915 -t IsSurface if ( $IsSurface ) then if ( 0 ) then set
Re: [Freesurfer] Error while using mri_glmfit
Hello experts, Could anyone provide me an advice or answer to this problem ? Thanks in advance ! Best regards, Matthieu Le 28 juil. 2015 14:12, Matthieu Vanhoutte matthieuvanhou...@gmail.com a écrit : Dear Freesurfer's Experts, Please find below an error occuring when I use mri_glmfit : Design matrix -- 1.000 0.000 0.000 0.000 0.000 0.000 9.804 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -10.612 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -21.114 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -12.936 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 15.129 0.000 0.000 0.000 0.000 0.000 17.562 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 16.402 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -6.889 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 10.584 0.000 0.000 0.000 0.000 0.000 37.017 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.243 0.000 0.000 0.000 0.000 0.000 7.675 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 20.432 0.000 0.000 0.000 0.000 0.000 43.865 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.287 0.000 0.000 0.000 0.000 0.000 23.719 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 10.735 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.734 0.000 0.000 0.000 0.000 0.000 21.167 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -8.197 0.000 0.000 0.000 0.000 0.000 -2.765 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -3.431 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -18.456 0.000 0.000 0.000 0.000 0.000 4.976; 1.000 0.000 0.000 0.000 0.000 0.000 -18.437 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.150 0.000 0.000 0.000 0.000 0.000 -1.417 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -16.936 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -3.442 0.000 0.000 0.000 0.000 0.000 21.991 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 9.298 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 6.360 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -17.536 0.000 0.000 0.000 0.000 0.000 1.896 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -19.658 0.000 0.000 0.000 0.000 0.000 -5.226 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.919 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 10.834 0.000 0.000 0.000 0.000 0.000 6.266 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.360 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.939 0.000 0.000 0.000 0.000 0.000 17.494 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -12.457 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -8.279 0.000 0.000 0.000 0.000 0.000 6.153; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 10.505 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 7.838 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000
Re: [Freesurfer] Error while using mri_glmfit
The Epilepsy_Duration is the same for all MaleControl subjects. You can't use that as a covariate if it does not have any variation On 08/04/2015 04:10 PM, Matthieu Vanhoutte wrote: Douglas, Please fond attached the fsgd file. Cheers, Matthieu Le 4 août 2015 21:45, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu a écrit : can you send the fsgd file? On 08/04/2015 03:42 PM, Matthieu Vanhoutte wrote: Hello experts, Could anyone provide me an advice or answer to this problem ? Thanks in advance ! Best regards, Matthieu Le 28 juil. 2015 14:12, Matthieu Vanhoutte matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com a écrit : Dear Freesurfer's Experts, Please find below an error occuring when I use mri_glmfit : Design matrix -- 1.000 0.000 0.000 0.000 0.000 0.000 9.804 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -10.612 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -21.114 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -12.936 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 15.129 0.000 0.000 0.000 0.000 0.000 17.562 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 16.402 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -6.889 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 10.584 0.000 0.000 0.000 0.000 0.000 37.017 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.243 0.000 0.000 0.000 0.000 0.000 7.675 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 20.432 0.000 0.000 0.000 0.000 0.000 43.865 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.287 0.000 0.000 0.000 0.000 0.000 23.719 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 10.735 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.734 0.000 0.000 0.000 0.000 0.000 21.167 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -8.197 0.000 0.000 0.000 0.000 0.000 -2.765 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -3.431 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -18.456 0.000 0.000 0.000 0.000 0.000 4.976; 1.000 0.000 0.000 0.000 0.000 0.000 -18.437 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.150 0.000 0.000 0.000 0.000 0.000 -1.417 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -16.936 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -3.442 0.000 0.000 0.000 0.000 0.000 21.991 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 9.298 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 6.360 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -17.536 0.000 0.000 0.000 0.000 0.000 1.896 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -19.658 0.000 0.000 0.000 0.000 0.000
Re: [Freesurfer] single hemisphere longitudinal analysis
You should just run it through with the other hemisphere even if the values are bogus. The aseg.stats file will not be produced until both hemis are done, but you can ignore anything that relates to the bad hemi. doug On 08/03/2015 11:36 AM, Andrea Horváth wrote: Dear Freesurfers, I tried to run recon-all on a single hemisphere. However, I only got the aparc stat files. Is it possible to get the aseg stats as well? Is it possible to do longitudinal analysis on a single hemisphere? We have big lesions in our patients in one of the hemispheres, so we would like to analyze the contralateral one. Thank you for your help in advance, Andrea ___ 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] Dimension mismatch between mask and run
Hi Doug, I deleted all of the template.nii files, and now the command works. Thank you for your advice! In regards to my other thread (selxavg3-sess error), where selxavg3 looks for a file that doesn't exist (fmcpr.sm5.nii.gz), could I rename the preproc-sess output volume (fmcpr.nii.gz) to fmcpr.sm5.nii.gz in order to run the command? Given preproc-sess at -fwhm 5, this volume should be smoothed at 5 and should be the input for analysis, correct? Thanks, Anais 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, August 04, 2015 3:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Dimension mismatch between mask and run There is still a warning about multiple formats. This means you have not deleted all the offending files. On 08/04/2015 12:19 PM, Rodriguez-Thompson, Anais wrote: Hi Doug, Thanks for getting back to me. I tried deleting those files, and got the same error, although the terminal output looked slightly different towards the end (in terms of the compensation values). Here it is below: -- selxavg3-sess logfile is /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_050514-150804121216.log -- preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_050514 -nolog -- preproc-sess logfile is /dev/null -- $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ arodthom setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a SIRP_LoadRegression_Stable5_050514 -nolog Tue Aug 4 12:12:17 EDT 2015 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 fmcpr mask 1 brain GDDA098 Template - mktemplate-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile -nolog -update Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Tue Aug 4 12:12:17 EDT 2015 Detected input format at nii GDDA098 Update not needed Run: 015 Tue Aug 4 12:12:17 EDT 2015 GDDA098 015 Update not needed Run: 016 Tue Aug 4 12:12:17 EDT 2015 GDDA098 016 Update not needed Run: 017 Tue Aug 4 12:12:17 EDT 2015 GDDA098 017 Update not needed Tue Aug 4 12:12:17 EDT 2015 mktemplate-sess completed GDDA098 Mask mkbrainmask-sess -maskstem brain -fsd bold -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 Tue Aug 4 12:12:17 EDT 2015 WARNING: multiple formats found for template USING: template.nii.gz GDDA098 Update not needed for session-level mask WARNING: multiple formats found for 015/template USING: 015/template.nii.gz GDDA098 Update not needed for run 015 mask GDDA098 Update not needed for run 015 meanval WARNING: multiple formats found for 016/template USING: 016/template.nii.gz GDDA098 Update not needed for run 016 mask GDDA098 Update not needed for run 016 meanval WARNING: multiple formats found for 017/template USING: 017/template.nii.gz GDDA098 Update not needed for run 017 mask GDDA098 Update not needed for run 017 meanval Tue Aug 4 12:12:18 EDT 2015 mkbrainmask-sess done GDDA098 Registration - register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update -- register-sess logfile is /dev/null -- Tue Aug 4 12:12:18 EDT 2015 setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun cd /autofs/cluster/roffman/users/Stable5_PerRun /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or directory Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098
Re: [Freesurfer] Error while using mri_glmfit
can you send the fsgd file? On 08/04/2015 03:42 PM, Matthieu Vanhoutte wrote: Hello experts, Could anyone provide me an advice or answer to this problem ? Thanks in advance ! Best regards, Matthieu Le 28 juil. 2015 14:12, Matthieu Vanhoutte matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com a écrit : Dear Freesurfer's Experts, Please find below an error occuring when I use mri_glmfit : Design matrix -- 1.000 0.000 0.000 0.000 0.000 0.000 9.804 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -10.612 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -21.114 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -12.936 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 15.129 0.000 0.000 0.000 0.000 0.000 17.562 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 16.402 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -6.889 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 10.584 0.000 0.000 0.000 0.000 0.000 37.017 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.243 0.000 0.000 0.000 0.000 0.000 7.675 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 20.432 0.000 0.000 0.000 0.000 0.000 43.865 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.287 0.000 0.000 0.000 0.000 0.000 23.719 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 10.735 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.734 0.000 0.000 0.000 0.000 0.000 21.167 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -8.197 0.000 0.000 0.000 0.000 0.000 -2.765 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -3.431 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -18.456 0.000 0.000 0.000 0.000 0.000 4.976; 1.000 0.000 0.000 0.000 0.000 0.000 -18.437 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.150 0.000 0.000 0.000 0.000 0.000 -1.417 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -16.936 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -3.442 0.000 0.000 0.000 0.000 0.000 21.991 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 9.298 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 6.360 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -17.536 0.000 0.000 0.000 0.000 0.000 1.896 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -19.658 0.000 0.000 0.000 0.000 0.000 -5.226 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.919 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 10.834 0.000 0.000 0.000 0.000 0.000 6.266 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.360 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.939 0.000 0.000 0.000 0.000 0.000 17.494 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -12.457 0.000 0.000 0.000 0.000 0.000 -15.576
Re: [Freesurfer] Error while using mri_glmfit
Douglas, Please fond attached the fsgd file. Cheers, Matthieu Le 4 août 2015 21:45, Douglas N Greve gr...@nmr.mgh.harvard.edu a écrit : can you send the fsgd file? On 08/04/2015 03:42 PM, Matthieu Vanhoutte wrote: Hello experts, Could anyone provide me an advice or answer to this problem ? Thanks in advance ! Best regards, Matthieu Le 28 juil. 2015 14:12, Matthieu Vanhoutte matthieuvanhou...@gmail.com mailto:matthieuvanhou...@gmail.com a écrit : Dear Freesurfer's Experts, Please find below an error occuring when I use mri_glmfit : Design matrix -- 1.000 0.000 0.000 0.000 0.000 0.000 9.804 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -10.612 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -21.114 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -12.936 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 15.129 0.000 0.000 0.000 0.000 0.000 17.562 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 16.402 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -6.889 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 10.584 0.000 0.000 0.000 0.000 0.000 37.017 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.243 0.000 0.000 0.000 0.000 0.000 7.675 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 20.432 0.000 0.000 0.000 0.000 0.000 43.865 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 5.287 0.000 0.000 0.000 0.000 0.000 23.719 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 10.735 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 3.734 0.000 0.000 0.000 0.000 0.000 21.167 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -8.197 0.000 0.000 0.000 0.000 0.000 -2.765 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -3.431 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -18.456 0.000 0.000 0.000 0.000 0.000 4.976; 1.000 0.000 0.000 0.000 0.000 0.000 -18.437 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.150 0.000 0.000 0.000 0.000 0.000 -1.417 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -16.936 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -3.442 0.000 0.000 0.000 0.000 0.000 21.991 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 9.298 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 6.360 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -17.536 0.000 0.000 0.000 0.000 0.000 1.896 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -19.658 0.000 0.000 0.000 0.000 0.000 -5.226 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 1.919 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000; 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 10.834 0.000 0.000 0.000 0.000 0.000 6.266 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 -2.360 0.000 0.000 0.000 0.000 0.000 -15.576 0.000 0.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 -1.939 0.000 0.000 0.000 0.000 0.000 17.494 0.000 0.000 0.000 0.000;
Re: [Freesurfer] qdec - Generate stats data table
Thank you this subject had a zip copy of the wmparc.statsNow I am missing this file from another subject. Do I need to run recon-all from start or is there a shortcut for getting this file?Thanks Doug.Pablo Date: Tue, 4 Aug 2015 11:42:43 -0400 From: gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] qdec - Generate stats data table Have you looked in /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats to see if there might be a problem? On 08/04/2015 05:43 AM, pablo najt wrote: Dear FS experts, I am trying to generate my stats data tables with QDEC -after successfully loading my data table- and come across the following error. Any recommendations would be greatly appreciated. Thank you in advance Pablo Data table loading completed successfully. SUBJECTS_DIR is '/Volumes/NEW_VOLUME/GBS' mkdir -p /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/ -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files Building the table.. Writing the table to /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/aseg.volume.stats.dat -- asegstats2table --common-segs --meas volume --tablefile /Volumes/NEW_VOLUME/GBS/qdec/stats_tables/wmparc.volume.stats.dat --statsfile=wmparc.stats --subjects 001ER 007JC 011GB 015NOK 018AM 022LH 041WVDP 045PC 054JB 058CS 062AH 070CDc 082MOHb 085CLa 090BC 093DC 095RA 100MOGc 103FC_6 108JMCM 117AS 121JB 137ED 156PMC 176VOD 181CD 188SL 192AL 214VH 229PK 240PE 246KF 258TOD 267OMCN 279SB 285SK 300VW 301EK 304CD 322MS 338JM 346FC_fep 352DFc 360PC 366BLh 383AW 387SD 389NM_first 393AGG 398JK 403SH 409MCa 414MOB 421JC 427LH 433MON 456MWb 461DC 464DDc 475GM 489MOC 492HGc 497RF 501POT 512EQ 532CC 561AGc 569AG 574BH 578DCa 582RG 585AOD 589JL 596JT 600MORb 605PS 615KS 620CB 624PW 635AG 650RCd 655PMCE 660AQ 668JG 673JK 699MOC 701TG 703MHc 711SJ 718PJ 732PS 736HODc 741JT 750MD 758JOLT 762MJ 777MCb 783DMCM 792GF 807YG 808MM 818NL 824MM 853MR 864AF 868ALF 872DCc 888MOB 896EF 905PG_5 914JB 917JH 923BOM 930TL 941MM 948SC 959FD 984PL 989OB 997SG SUBJECTS_DIR : /Volumes/NEW_VOLUME/GBS Parsing the .stats files ERROR: The stats file /Volumes/NEW_VOLUME/GBS/117AS/stats/wmparc.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files ___ 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
