Freesurfer February 2016

freesurfer@nmr.mgh.harvard.edu

123 participants
179 discussions

generate .mgz file from DICOM
by Kan Ding 07 Feb '16

07 Feb '16

Hi, I am having trouble to generate .mgz file from DICOM. However, I was able to run the same code with NIFTI file. What did I do wrong? Thanks for your help. Kan NUA502608:300T1 kding$ ls 30100000-0.dcm 30100000-27.dcm 30100000-1.dcm 30100000-28.dcm 30100000-10.dcm 30100000-29.dcm 30100000-100.dcm 30100000-3.dcm 30100000-101.dcm 30100000-30.dcm 30100000-102.dcm 30100000-31.dcm 30100000-103.dcm 30100000-32.dcm 30100000-104.dcm 30100000-33.dcm 30100000-105.dcm 30100000-34.dcm 30100000-106.dcm 30100000-35.dcm 30100000-107.dcm 30100000-36.dcm 30100000-108.dcm 30100000-37.dcm 30100000-109.dcm 30100000-38.dcm 30100000-11.dcm 30100000-39.dcm 30100000-110.dcm 30100000-4.dcm 30100000-111.dcm 30100000-40.dcm 30100000-112.dcm 30100000-41.dcm 30100000-113.dcm 30100000-42.dcm 30100000-114.dcm 30100000-43.dcm 30100000-115.dcm 30100000-44.dcm 30100000-116.dcm 30100000-45.dcm 30100000-117.dcm 30100000-46.dcm 30100000-118.dcm 30100000-47.dcm 30100000-119.dcm 30100000-48.dcm 30100000-12.dcm 30100000-49.dcm 30100000-120.dcm 30100000-5.dcm 30100000-121.dcm 30100000-50.dcm 30100000-122.dcm 30100000-51.dcm 30100000-123.dcm 30100000-52.dcm 30100000-124.dcm 30100000-53.dcm 30100000-125.dcm 30100000-54.dcm 30100000-126.dcm 30100000-55.dcm 30100000-127.dcm 30100000-56.dcm 30100000-128.dcm 30100000-57.dcm 30100000-129.dcm 30100000-58.dcm 30100000-13.dcm 30100000-59.dcm 30100000-130.dcm 30100000-6.dcm 30100000-131.dcm 30100000-60.dcm 30100000-132.dcm 30100000-61.dcm 30100000-133.dcm 30100000-62.dcm 30100000-134.dcm 30100000-63.dcm 30100000-135.dcm 30100000-64.dcm 30100000-136.dcm 30100000-65.dcm 30100000-137.dcm 30100000-66.dcm 30100000-138.dcm 30100000-67.dcm 30100000-139.dcm 30100000-68.dcm 30100000-14.dcm 30100000-69.dcm 30100000-140.dcm 30100000-7.dcm 30100000-141.dcm 30100000-70.dcm 30100000-142.dcm 30100000-71.dcm 30100000-143.dcm 30100000-72.dcm 30100000-144.dcm 30100000-73.dcm 30100000-145.dcm 30100000-74.dcm 30100000-146.dcm 30100000-75.dcm 30100000-147.dcm 30100000-76.dcm 30100000-148.dcm 30100000-77.dcm 30100000-149.dcm 30100000-78.dcm 30100000-15.dcm 30100000-79.dcm 30100000-150.dcm 30100000-8.dcm 30100000-151.dcm 30100000-80.dcm 30100000-152.dcm 30100000-81.dcm 30100000-153.dcm 30100000-82.dcm 30100000-154.dcm 30100000-83.dcm 30100000-155.dcm 30100000-84.dcm 30100000-156.dcm 30100000-85.dcm 30100000-157.dcm 30100000-86.dcm 30100000-158.dcm 30100000-87.dcm 30100000-159.dcm 30100000-88.dcm 30100000-16.dcm 30100000-89.dcm 30100000-160.dcm 30100000-9.dcm 30100000-17.dcm 30100000-90.dcm 30100000-18.dcm 30100000-91.dcm 30100000-19.dcm 30100000-92.dcm 30100000-2.dcm 30100000-93.dcm 30100000-20.dcm 30100000-94.dcm 30100000-21.dcm 30100000-95.dcm 30100000-22.dcm 30100000-96.dcm 30100000-23.dcm 30100000-97.dcm 30100000-24.dcm 30100000-98.dcm 30100000-25.dcm 30100000-99.dcm 30100000-26.dcm NUA502608:300T1 kding$ recon-all -i 30100000-0.dcm -s 300 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/kding/desktop/data/TBIE/TBIET1/300T1 Actual FREESURFER_HOME /Applications/freesurfer Darwin nua502608.dhcp.swmed.org 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 /Users/kding/desktop/data/TBIE/TBIET1/300T1/300 \n mri_convert /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm /Users/kding/desktop/data/TBIE/TBIET1/300T1/300/mri/orig/001.mgz \n mri_convert /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm /Users/kding/desktop/data/TBIE/TBIET1/300T1/300/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm... Starting DICOMRead2() dcmfile = /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm dcmdir = /Users/kding/desktop/data/TBIE/TBIET1/300T1 WARNING: tag ImageNumber not found in /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm WARNING: tag image orientation not found in /Users/kding/desktop/data/TBIE/TBIET1/300T1/30100000-0.dcm Ref Series No = 18976 ERROR: bits = 0 not supported. Send email to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Darwin nua502608.dhcp.swmed.org 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 recon-all -s 300 exited with ERRORS at Thu Feb 4 15:53:19 CST 2016 For more details, see the log file /Users/kding/desktop/data/TBIE/TBIET1/300T1/300/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Volume analysis in native space vs. mni305 space
by Rodriguez-Thompson, Anais 07 Feb '16

07 Feb '16

Hi FreeSurfer experts, I'm in the process of switching over our first-level analyses from being run in native space to being run in fsaverage/mni305 space. Looking at the first-levels on an individual subject level, the volume analyses look fairly different (cortical signal especially is lost in the mni305 analysis). I've attached a couple of slides with images comparing the two volume analyses. My commands for the mni305 analysis are... Pre-processing: preproc-sess -s GDDA001 -surface fsaverage lhrh -mni305 -fwhm 5 -per-run -d $SUBJECTS_DIR -fsd bold -so siemens Mkanalysis: mkanalysis-sess -analysis SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -mni305 2 -fwhm 5 -paradigm slopepar -event-related -fsd bold -runlistfile runlistfile -tpef tpef_1.5mm.txt -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 -per-run -TR 2 -stc siemens -force Mkcontrast: mkcontrast-sess -analysis SIRP_LoadRegression_Stable5.3_012616_sm5_mni305 -contrast 2vFix -a 2 -c 0 My commands for the native space analysis are... Preprocessing: preproc-sess -s GDDA001 -fwhm 5 -per-run -d $SUBJECTS_DIR -fsd bold Mkanalysis: mkanalysis-sess -analysis SIRP_LoadRegression_Stable5_050514 -TR 2 -paradigm slopepar -event-related -runlistfile runlistfile -tpef tpef_1.5mm.txt -native -fwhm 5 -timewindow 20 -TER 2 -nconditions 9 -gammafit 2.25 1.25 -refeventdur 2 Mkcontrast: mkcontrast-sess -analysis SIRP_LoadRegression_Stable5_050514 -contrast 2vFix -a 2 -c 0 I have a couple of questions regarding the differences between the two analyses. First, why is so much of the signal robustness from the native space volume analysis lost in the mni305 analysis? Second, why are the voxel sizes so different between the two analyses (with the native space analysis having a much larger voxel size)? Thanks, Anais

2 2

spot checking results
by Krieger, Donald N. 07 Feb '16

07 Feb '16

Dear List, I have run recon-all -all on the same scan on two different machines likely running two different versions of Linux but in any case the runs were done with different numbers of cores. I haven't done anything fancy to compare that the results are identical except for some spot checks of individual files with md5sum. label/lh.BA4a.label shows up the same on both. mri/wmparc.mgz does not. Your comments would be welcome. Is there something about the non-ascii files, e.g. wmparc.mgz, which would make them show different checksums, e.g. inclusion of a processing time or some such? Do you have experience or suggestions for convincing ourselves that we are getting the same answers on different machines? ??? Thanks - Don

3 2

To use a ROI.label as seed in FS-FAST
by stdp82＠virgilio.it 07 Feb '16

07 Feb '16

Hi list, I would like to use as seed in FS-FAST a ROI.label which I have drawn on a cluster in tksurfer.How can I do it?Should I use mri_label2vol? Thanks. Stefano

2 1

Paired analysis FSFAST
by Thục Trinh 07 Feb '16

07 Feb '16

Hello, I'm working on group analysis in fMRI activation using FSFAST. I tend to test whether any significant changed in fMRI activation within group across two time points ( pre-training vs post). I ran first level already. I still confuse about the concat data and the mri_glmfit command. Here are the command lines, I'm wondering if it runs exactly what I want it to do. -- idlist Input NCP140005_1 Input NCP140005_2 Input NCP140012_1 Input NCP140012_2 Input NCP140071_1 Input NCP140071_2 Input NCP140079_1 Input NCP140079_2 Input NCP140082_1 Input NCP140082_2 Input NCP140543_1 Input NCP140543_2 Input NCP140556_1 Input NCP140556_2 Input NCP140558_1 Input NCP140558_2 -- concat data isxconcat-sess -sf idlist -analysis work.sm5.lh -contrast con-v-arrow -o group2 -- FSGD file GroupDescriptorFile 1 Title Con-arrow Gr2 Class Defi Input NCP140005 Defi Input NCP140012 Defi Input NCP140071 Defi Input NCP140079 Defi Input NCP140082 Defi Input NCP140543 Defi Input NCP140556 Defi Input NCP140558 Defi -- run glm analyisis mri_glmfit --glmdir lh.paired.gr2-diff --y ces.nii --fsgd con-arrow_group2.fsgd --C mean.mat -- content in matrix contrast C = [ 1 0 ] Thank you, Trinh

2 1

Planum temporale measurement
by Adam David Felton 07 Feb '16

07 Feb '16

Hello, I checked the listserv history, but couldn't find an answer to my question: With the 2009 parcellation scheme, 1) does the planum temporale parcellation include the posterior ascending ramus (which Destrieux et al. 2010 seems to imply) and 2) does the planum temporale include the posterior descending ramus? Thank you! Adam

3 2

Freesurfer v6.0 + edit in v5.3.0 then rerun v6.0
by Tiril Pedersen Gurholt 06 Feb '16

06 Feb '16

Dear Freesurfer Experts, It is my understanding that Freesurfer v6.0 is at the verge of being released. Do you have a tentative v6.0 release data? Also, there is a beta version of Freesurfer v6.0. How stable is it? (Mostly thinking of the recon-all pipeline.) Some of our data has been processed in Freesurfer v5.3.0 (recon-all to structural T1 data) and then manually edited. Is there a downside to rerun this data processed in v5.3.0 (after manual edit) in v6.0? Or is it best (or advisable) to rerun this data from the original T1 data in v6.0 and then do a new round of manual edit? Best regards, Tiril ?? -- Tiril Gurholt Postdoctoral Fellow - Psychosis Research Centre University of Oslo, Norway

2 1

seq.info
by Ji Won Bang 05 Feb '16

05 Feb '16

Dear. Freesurfer team I used dcmunpack to convert DCM to nii. This command didn't generate seq.info (I couldn't find it). I'd like to create one by myself.... Do you know how I can check the scan parameters: sequencename nrows ncols nslcs rowpixelsize colpixelsize slcpixelsize ntrs TR I know that when I use: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir /scan.info I can get sequencename, nrows, ncols... but then from where can I check the others? Thank you very much. Best, Ji Won

2 3

DTI - Tracula question
by Alan Francis 05 Feb '16

05 Feb '16

Hi Anastasia: I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single nii.gz file. The BVECS and BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file? Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS? thank you so much, best regards, Alan -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* NIDA T32 Fellow in Computational Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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Re: [Freesurfer] TRACULA Longitudinal can't find subject folder
by Deniz Gursel 05 Feb '16

05 Feb '16

Dear Anastasia, Thank you very much for your fast solution. Indeed, I was missing the related folders, I haven’t run the recon-all myself and I copied only the final folder and not the whole as a mistake. Now, I passed that error and got stuck with a new one. In the inter-subject registration step, I get the error: #@# Image corrections Fri Feb 5 14:34:25 CET 2016 mri_convert /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz mri_convert /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /data_august/Deniz/DTI_long/subjects/med_AhJa94_2.long.med_AhJa94/dwi.nii... crypt_gkey = FS1gOHzYgoG2U TR=10443.18, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998789, 0.0474208, 0.0131247) j_ras = (0.0473438, 0.99886, -0.00611764) k_ras = (0.0133998, 0.00548885, 0.999895) writing to /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_2.long.med_AhJa94/dmri/dwi_orig.nii.gz... crypt_gkey = FS1gOHzYgoG2U if: Expression Syntax. #------------------------------------- /sw/freesurfer/5.3.0/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Fri Feb 5 14:34:30 CET 2016 cp /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat /data_august/Deniz/DTI_long/traculaoutput/med_AhJa94/dmri/xfms cp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/mni2anatorig.mat’: No such file or directory cp: cannot stat ‘/data_august/Deniz/DTI_long/traculaoutput/med_AhJa94_1.long.med_AhJa94/dmri/xfms/anatorig2mni.mat’: No such file or directory Linux slow.mri.tu-muenchen.de 3.7.10-1.40-desktop #1 SMP PREEMPT Thu Jul 10 11:22:12 UTC 2014 (9b06319) x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Feb 5 14:34:30 CET 2016 I am attaching the trac_all.log, trac_all.error and dmrirc for you. Also, before the error, at the image correction step, there is “if: expression syntax” message which I couldn’t figure out why it happens. I looked it up and seems like some Unix error. I encountered it many times, when I was running another cross-sectional study and sometimes it went away magically. Thank you very much for your time and help.

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Freesurfer February 2016