Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30090 discussions

PetSurfer GTM: gtmstats2table
by Elijah Mak 12 Sep '17

12 Sep '17

Hi Doug, Would it be possible to use the gtmstats2table command to extract GTM values from other parellations? Thanks! Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities Research Group University of Cambridge, Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24

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lobes volume (WM and GM)
by Gonzalo Rojas Costa 12 Sep '17

12 Sep '17

Hi: I need the complete WM volume for each lobe... not only the WM up to 5mm beneath the lobes (default value) or 20 mm... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oAAAAJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta

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lobes volume (WM and GM)
by Gonzalo Rojas Costa 12 Sep '17

12 Sep '17

Hi: I created the following script (for freesurfer 5.3.0) to compute the lobes volume (including GM and WM). mri_annotation2label --subject pac --hemi rh --lobesStrict lobulos --seg lobulos --stat lobulos mri_annotation2label --subject pac --hemi lh --lobesStrict lobulos --seg lobulos --stat lobulos mris_anatomical_stats -a lobulos -f pac.lobulos.rh pac rh mris_anatomical_stats -a lobulos -f pac.lobulos.lh pac lh mri_aparc2aseg --s pac --labelwm --hypo-as-wm --rip-unknown --volmask --o $SUBJECTS_DIR/pac/mri/lobulitos.mgz --annot lobulos --wmparc-dmax 20 mri_segstats --seg $SUBJECTS_DIR/pac/mri/lobulitos.mgz --ctab /usr/local/freesurfer/LobulesColorLUT.txt --excludeid 0 --sum $i.lobulo.aseg.sum --id 1001 1004 1005 1006 2001 2004 2005 2006 3001 3004 3005 3006 4001 4004 4005 4006 251 252 253 254 255 But, I didn't got the complete WM volume for each lobe (frontal lobe for example... see red arrow in attached image)... why ?... Any solution ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl http://www.aribrain.info https://scholar.google.com/citations?user=LO7LZ3oAAAAJ https://www.researchgate.net/profile/Gonzalo_Rojas2 https://cl.linkedin.com/in/gonzalorojascosta

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QDEC FDR for left and right hemispheres
by Huang, Caleb (NIH/NINDS) [F] 12 Sep '17

12 Sep '17

Hello, When I run FDR on QDEC, I get different p-values for the left and right hemispheres. Is it appropriate to use just one threshold for the sake of consistency? Also, as an unrelated question, is there a way to display the thresholds as p-values rather than log(p)? -Caleb

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side effects launching recon-all from matlab system(cmd) call
by Giuseppe Cabras 12 Sep '17

12 Sep '17

Dear freesurfer developers, I call recon-all -all from a matlab script using a system(cmd) which is (apparently) correctly executed, as shown in the recon-all.log (matlab_* attached), i.e.: /usr/local/freesurfer/bin/recon-all -all -cw256 -3T -multistrip -clean-bm -i /home/MRIdata/PUD/31148_MRI_sMRI_400614.nii -s /home/gc/study/recon-all/400614dclass and apparently it run without errors as you can see in the matlab_recon-all.log file, but I get (systematically) a wrong TalAviQA: 0.00000 while, if I run the above bash command directly I get a correct: TalAviQA: 0.97713 as shown in the bash_recon-all.log (attached). I guessed that something wrong happened in talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig and the error traced in talairach_avi.log (matlab_* and bash_* attached). In fact matlab_talairach_avi.log is shorter and all imgreg_4dfp end sections are missing which imply that TalAviQA can not be extracted by awk and mritotal transform is performed instead. But really I don't understand why this happens and whether similar issues affects other recon-all subtask using matlab. I double checked this on two linux sistems and with fs version 6.0 and 5.3 ... same results. Thanks in advance for any help, cheers, -- Giuseppe Cabras, PhD - Department of Mathematics, Computer Science and Physics InterUniversity Center for Behavioral Neurosciences University of Udine - via delle Scienze, 206 - 33100 UDINE

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FS6.0 on RHEL7 FIPS enabled - ERROR: crypt() returned null with 4-line file
by Sean T. Ma 12 Sep '17

12 Sep '17

Hi FS experts, I ran into a crypt() error while running the `recon-all` on a test brain with Freesurfer 6.0 installed. The server is an FIPS enabled RHEL7. In the `recon-all.log`, the error happened after the `mri_convert.bin` execution: ERROR: crypt() returned null with 4-line file I have attached a snippet below as well as the recon-all.log. Has anyone encountered this error before? I'm suspecting the issue might be due to the enabling of FIPS on RHEL7. I'm having similar OpenSSL prolembs in FSL/FSLeyes. Your input is appreciated! Best, Sean mri_convert /nfs/fmri/Analysis/FSinputs/test/t1spgr_156sl.nii /nfs/fmri/Analysis/FSresults/test/mri/orig/001.mgz mri_convert.bin /nfs/fmri/Analysis/FSinputs/test/t1spgr_156sl.nii /nfs/fmri/Analysis/FSresults/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /nfs/fmri/Analysis/FSinputs/test/t1spgr_156sl.nii... ERROR: crypt() returned null with 4-line file Linux madcbrain.umms.med.umich.edu 3.10.0-693.el7.x86_64 #1 SMP Thu Jul 6 19:56:57 EDT 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s test exited with ERRORS at Wed Sep 6 12:01:48 EDT 2017

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do I need to re-ROI the segmentation after recon-all
by shi yao wang 12 Sep '17

12 Sep '17

Dear FS experts: After I finishing recon-all, do I need to check the segmentation and re-roi some of region? thanks Lawrence Emory University

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(no subject)
by yl88＠nyu.edu 12 Sep '17

12 Sep '17

Hi all, I have finished the command “recon -all” without error. But I get an error that says: “Received X error! Error code :158 Request code : 148 Minor code: 2 Error text :’GLXBadLargeRequest’” I am using the command “tksurfer sub lh inflated”. Then clicking the File->Label->load label.-> and choosing document of “the lh.apare.a2009.annot”. I don’t know why I got this error so would you be able to explain why this is the case and how I can go about resolving this problem? Best, Yvonne

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automatic quality control in freesurfer
by shi yao wang 12 Sep '17

12 Sep '17

Dear FS experts: Just wondering if there were any automatic method to perform quality control especially for segmentation. thanks Lawrence

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Talairach registration error
by Ariana Vajdi 11 Sep '17

11 Sep '17

Hello, Hope this message finds you well. I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountered this error before here and there, but I've been receiving the same error for every scan that I've been trying to run, and I'm not sure why. It's also the first time I've used NIFTI files as the input - not sure if that's a contributing factor. I've also tried the -use-mritotal flag without any luck. These are the errors I receive: WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. I would appreciate your help. Thank you! Warmly, Ariana

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