[Freesurfer] Ask question about QAtools
Dear Freesurfer experts, I installed the QAtools and tried a subject with this commond: $QA_TOOLS/recon_checker -s sub13 -snaps-detailed -gen-asegLUT aseglut.txt but I encountered the following Error message, can someone help me figure it out? Any help is appriciated, thanks! Error message 1: Received X error! error code : 1 request code : 148 minor code : 179 Error text: 'BadRequest (invalid request code or no such operation)' Error message 2: /opt/fmritools/QAtools/takesnapshotpreset.sh : line 89: convert: command not found both of the above two error messages shown in the screen many times, and there was no figures in the 'QA_check.html' Is it because I didn't install QAtools correctly? and what should I do? By the way, I do not have solid anatomical background, is it acceptable that I only use QAtools for quality control, without manual editing? I am thinking manual editing by non-experts will induce incorrect data. Any suggestion? Thanks a lot! 2012-03-05 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 ___ 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] save custom made path on surface as label
Dear freesurfer experts, I draw a path with the tksurfer tools on a surface, but was not able to save this path as a label. During the custom fill step it marked the whole surface and not just the path. I think it is because the path is not closed. Is there still a way to get a path as a label file? cheers, erhan -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax:+49 (69) 96769-327 e-mail: g...@mpih-frankfurt.mpg.de http://www.brain.mpg.de/research/singer-emeritus-department/people/erhan-genc/ ___ 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] Output volume along with its calculated pia
Hi Octavian try using mris_fill with the pial surface to generate a binary volume that is 1 in the interior of the pial and 0 outside of it. cheers Bruce On Sun, 4 Mar 2012, octavian lie wrote: Dear All, I am increasingly fascinated by freesurfer. Here is a rookie issue: I use a source imaging program that is rather simple-minded in its MRI processing steps. To be able to use the inverse solution tools of that program, I need to use 2 volumes: - a head MRI to be used to electrode coregistration - a skull-stripped brain MR without cerebellum, including both the gray and white matter; the program needs to perform its own white matter extraction to generate the gray matter volume to be used as source space. - both MRs have to be subject to the same transforms, if any, and have to have the same origin and coordinate systems (like real head/brain pairs). So first, I am in the search of the best brain extraction possible, with as little dura included as possible. Besides trying to implement Andre's dura protocols, and editing the pial surface for brainmask.mgz, then running the rest of the recon-all steps, I need to be able to export in nii.gz format a volume having its pial surface as calculated by freesurfer. When exporting brain.finalsurfs.mgz with mri_convert, it looks that the calculated pial surface as visualized with tkmedit subjid brain.finalsurfs.mgz -surfs is ignored in the nii.gz file. When the output nii volume is imported in programs such as Bioimage Suite, I essentially see what looks like the outside (surface) brainmask.mgz volume as in tekmedit but not accounting for the calculated pial surface. How can I export brain.finalsurfs.mgz with its calculated pial surface as a nii volume? In other words, I would need a ribbon.mgz type volume to include the white matter on the inside. I suppose it comes down to adding options to the mri_convert brain.finalsurfs.mgz step after surfaces have been generated, but I would need some guidance Please advise. Octavian. ___ 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] Help! What does the error mean
can you run mri_info /home/wb/test_data/ZWK/34810194 and send us the results? It will probably tell you that that volume has multiple frames, so the next question is why? What acquisition are you using? cheers Bruce On Mon, 5 Mar 2012, bowan...@mail.ustc.edu.cn wrote: Dear All I was just process the commands: recon-all -i /home/wb/test_data/ZWK/34810194 \ -s ZWK \ -sd /home/wb/test/ \ -all And then Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! I just want to know what does the error mean? Yours BoBO ___ 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] Coordinates of output files
The nifti qform should be that of the scanner. doug octavian lie wrote: Dear All, I am using a pipeline for electrode coregistration including freesurfer for pial surface generation, run by default recon-all -all and mris_volmask with --save_distance option. The FS files ?h.dpial.ribbon.mgz are the sole FS output. They are converted in the pipeline to nii.gz files using the mri_convert with no specific flags. Question, what coordinate system is used in the converted nii.gz file: a native/scan system, FS system, talairach system (after several recon-all steps of talairach transformation), or NIFTI system? Is there a way to call a command to confirm the exact system used? Thank you, Octavian. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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] aseg segmentation problem
wow, that's pretty bad. We haven't seen that in a while. What version are you running? If you upload the subject I'll take a look Bruce On Mon, 5 Mar 2012, Margaret Sheridan wrote: Hi all, I know on principle the aseg is not supposed to be edited but we have a case (attached) where the segmentation is quite good (and the MPRAGE looks fine) but the hippocampus has been mislabeled as cortex. How should I go about re-assigning this label? Thanks! Margaret ___ 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] -mprage flags
Hi all, What does -washu_mprage and -mprage flags do in autorecon step. How does it help in segmentation? -SK ___ 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] -mprage flags
it changes some of the assumptions about CNR and SNR. Bascially, the mprage has higher CNR and lower SNR than FLASH/SGPR, so for example when we are doing region growing to find control points the -mprage switch will ue a higher threshold to allow the control points to grow more liberally than in general On Mon, 5 Mar 2012, Sabin Khadka wrote: Hi all, What does -washu_mprage and -mprage flags do in autorecon step. How does it help in segmentation? -SK ___ 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] Create summary images
Hi Charlotte, With these scripts you can take snapshots of the aseg for several subjects in tkmedit. I'd suggest including the -snaps-detailed flag to get a large sample of slices from the aseg. https://surfer.nmr.mgh.harvard.edu/fswiki/QATools -Louis On Fri, 2 Mar 2012, Bruce Fischl wrote: yes, I think Louis has some code for facilitating this On Fri, 2 Mar 2012, Charlotte Bernard wrote: Dear Freesurfer users, I would like to know if it is possible to quickly inspect subcortical structure segmentation quality on a large number of subjects. I have read a post on that topic but i am not sure I understand how to process. Could you give a command line to do that? Thanks a lot, Charlotte ___ 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 Error in analyze: command failed
Hi, I'm getting an error in analyze: command failed: mri_concat notification when trying to run qdec on a within subjects analysis (N=29, looking at thickness and social functioning whilst controlling for ICV). I'm not sure what this means. See the output below. Thanks! Laura. Data table loading completed successfully. SUBJECTS_DIR is '/ncf/snp/04/SCORE/freesurfer_analysis' lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? Nuisance factors: ICV_Mean_Centered 1.000 0.000 0.000; lh-Avg-thickness-Social_Fx-Cor --- Does the correlation between thickness and Social_Fx differ from zero? Nuisance factors: ICV_Mean_Centered 0.000 1.000 0.000; sh: ICV/y.mgh: No such file or directory ninputs = 29 Checking inputs nframestot = 29 Allocing output Done allocing nframes = 29 Writing to /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx unknown file type for file (/ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFx) Error in Analyze: command failed: mri_concat /ncf/snp/04/SCORE/freesurfer_analysis/27119/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27120/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27121/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27122/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27125/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27127/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27131/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27140/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27145/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27160/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27164/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27191/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27193/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27194/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27195/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27196/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27199/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27201/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27203/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27204/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27205/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27206/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27208/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27210/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27211/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27212/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27213/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27216/surf/lh.thickness.fwhm10.fsaverage.mgh /ncf/snp/04/SCORE/freesurfer_analysis/27218/surf/lh.thickness.fwhm10.fsaverage.mgh --o /ncf/snp/04/SCORE/freesurfer_analysis/qdec/lh_thick_10_HC_SocFxICV/y.mgh -- Laura Tully Social Neuroscience Psychopathology Harvard University 840 William James Hall 33 Kirkland St Cambridge, MA 02138 ltu...@fas.harvard.edu ___ 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] pwd: permission denied
Hi, I am new to FS and have encountered a weird problem that I do not know how to solve and did not find any earlier postings on. When I run recon-all on a file in my own home directory everything works normally: recon-all -subject BIG1026_1 -sd /home/mrphys/marzwi/test -i BIG1026_1.nii.gz -autorecon1 [..] However, if I run the same command on the same file, except that this file is now located in a directory of a colleague of mine that I certainly have full access to (+r+w+x), I immediately get a 'permission denied' error: recon-all -subject BIG1026_1 -sd /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness -i BIG1026_1.nii.gz -autorecon1 pwd: cannot open directory `../..': Permission denied /bin/pwd: cannot open directory `../..': Permission denied mkdir: cannot create directory `/BIG1026_1': Permission denied [..] From the error message it seems to me as if FS is trying to access the parent directory (of which I do not have full rights but only -r-w+x)? As this does not make a lot of sense to me I suspect there must be another cause and hope you have any ideas here. Cheers, Marcel -- Marcel Zwiers www.ru.nl/donders MR techniques +31-(0)24-3668495 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands ___ 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] controls points in 5.1
Bruce, You had posted that there is a 'backwards compatibility flag' regarding control points manually specified to the aseg normalization in Freesurfer version 5.1 (see your thread from 1/27/12 below). You said that Nick might know about this flag. I too had noticed very different behavior after adding control points in v5.0 and v5.1, as many more regions were tagged as white matter in v5.1 than in v5.0. Would anyone know if this flag exists and how to use it? Thanks, Chris Re: [Freesurfer] control point guidanceBruce Fischl Fri, 27 Jan 2012 11:58:38 -0800 Hi Mikeit's a bit hard to state the region of effect for the control points. Essentially we go through and label voxels as control points or not based on their intensity, intensity gradient and connectivity (that is, the must be 6-connected to other control points) then build a Voronoi diagram and each control point sets the scaling for its Voronoi triangle. Thus if you have a control point surrounded by others its region of effect is small, but one control point all by itself can have a large region of effect.Also, 5.1 applies the manually specified control points to the aseg normalization (norm.mgz), whereas older versions didn't. Not everyone is happy with this, so I think there is a backwards compatibility flag. Nick would know.Bruce ___ 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] mri_vol2surf error writing to nifti volume
Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing SetSlice $gnVolSlice [set gnVolSlice] invoked from within .w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke (uplevel body line 1) invoked from within uplevel #0 [list $w invoke] (procedure tk::ButtonUp line 22) invoked from within tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc (command bound to event) UT Southwestern Medical Center The future of medicine, today. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] (no subject)
Hello all, I'm encountering a problem when I try to compare two timepoints for a particular subject. I run the command recon-all -all -s 7107-46-tp1 -i 7107-46-1/001.mgz and the end of the output stream where I receive errors shows the following below. Any help is greatly appreciated! painting output onto subject 7107-46-tp1. processing subject lh.EC_average... MRISread(/media/raid/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /media/raid/freesurfer/subjects/lh.EC_average/surf/lh.sphere.r$ Too many levels of symbolic links Linux mriserver.archlab 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 7107-46-tp1 exited with ERRORS at Sat Feb 25 02:34:14 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -Ryan ___ 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] (no subject)
Hi Ryan what is your SUBJECTS_DIR? You probably want it to be somewhere other than $FREESURFER_HOME/subjects as it is trying to create a symlink. cheers Bruce On Mon, 5 Mar 2012, Ryan wrote: Hello all, I'm encountering a problem when I try to compare two timepoints for a particular subject. I run the command recon-all -all -s 7107-46-tp1 -i 7107-46-1/001.mgz and the end of the output stream where I receive errors shows the following below. Any help is greatly appreciated! painting output onto subject 7107-46-tp1. processing subject lh.EC_average... MRISread(/media/raid/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /media/raid/freesurfer/subjects/lh.EC_average/surf/lh.sphere.r$ Too many levels of symbolic links Linux mriserver.archlab 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 7107-46-tp1 exited with ERRORS at Sat Feb 25 02:34:14 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -Ryan ___ 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] Ask question about QAtools
Dear Freesurfer experts, I installed the QAtools and tried a subject with this commond: $QA_TOOLS/recon_checker -s sub13 -snaps-detailed -gen-asegLUT aseglut.txt but I encountered the following Error message, can someone help me figure it out? Any help is appriciated, thanks! Error message 1: Received X error! error code : 1 request code : 148 minor code : 179 Error text: 'BadRequest (invalid request code or no such operation)' Error message 2: /opt/fmritools/QAtools/takesnapshotpreset.sh : line 89: convert: command not found both of the above two error messages shown in the screen many times, and there was no figures in the 'QA_check.html' By the way, I do not have solid anatomical background, is it acceptable that I only use QAtools for quality control, without manual editing? I am thinking manual editing by non-experts will induce incorrect data. Any suggestion? Thanks a lot! 2012-03-05 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 ___ 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.
