[Freesurfer] tracula error message
Hi Freesurfers, Could you help me interpret this error message? I am attempting to run TRACULA using version 6 on a MacBook Pro OS X El Capitan Version 10.11.3 helpdesks-MacBook-Pro-2:R01_DTI crc$ trac-all -prep -c dmrirc.example1 INFO: SUBJECTS_DIR is /Users/crc/Documents/myprojects/R01_DTI INFO: Diffusion root is /Users/CRC/Documents/myprojects/R01_DTI/tracresults Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/dmrirc.local -log /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/trac-all.log -cmd /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/scripts/trac-all.cmd #- /Applications/freesurfer/bin/trac-preproc #- #@# Image corrections Fri Jul 21 09:28:12 EDT 2017 mri_convert --bvec-voxel /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/nifty.nii.gz... TR=3222.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.997757, 0.0345085, 0.057362) j_ras = (0.0453079, 0.978915, 0.19918) k_ras = (0.0492791, -0.201332, 0.978283) writing to /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz... cp /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/bvec /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvecs cp /Users/CRC/Documents/myprojects/R01_DTI/NAH001-1/DTI/bval /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvals mv -f /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/bvecs.tmp /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvecs mv -f /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/bvals.tmp /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.bvals orientLAS /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig.nii.gz /Users/CRC/Documents/myprojects/R01_DTI/tracresults/NAH001-1/dmri/dwi_orig_las.nii.gz dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Trace/BPT trap ERROR: input file must be in NIfTI format Darwin helpdesks-MacBook-Pro-2.local 15.3.0 Darwin Kernel Version 15.3.0: Thu Dec 10 18:40:58 PST 2015; root:xnu-3248.30.4~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Jul 21 09:29:59 EDT 2017 helpdesks-MacBook-Pro-2:R01_DTI crc$ It says at the end that the input file needs to be in nifty format, but my input file is in nifty format. Do you guys have any idea what could be going on here. I attached my dmrirc.example file for your reference as well. Thank you, Marissa dmrirc.example1 Description: Binary data ___ 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] bvals and bvecs for tracula v6
Hi freesurfers, I recently updated my freesurfer version from 5.3 to 6, and I'm running into a problem with the tracula dmrirc.example file. In the dmrirc.example file for v5.3, it required just the bvals and bvecs in a text file in the correct format. For v6, it now requires a bval files, bval list, bvec file and bvec list. Could you give me an example of what the bval list and bvec list would look like? I'm not sure what the difference is, and I've tried a few different things but cannot get tracula to run correctly due to there being an error with these inputs. Marissa ___ 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] Analyzing xhemi results
Hi free surfers, I have run the xhemi process on the subjects for my study. The study is on stroke patients and their lesions are a mix of left and right hemispheres. In analyzing the results, we want to look at correlations between fmri activation in M1 and the cortical thickness of M1 ipsilesional and contralesional. To do so, I followed instructions written out in response to a question about xhemi on the mailing list: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-December/026823.html My question, is there a way when running the analysis step: *# Analyze *>* mri_glmfit --y lh.lh-rh.thickness.sm05.mgh --glmdir *>* glm.lh.lh-rh.thickness.sm05 \ *>* --osgm --surf fsaverage_sym lh *> Can I modify this command line to include my fmri data and run that correlation also? Thank you, Marissa ___ 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] xhemi label
Hi Doug, I'm not sure how to use this binary. Do I need to install it? Marissa On Fri, Mar 17, 2017 at 12:23 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > Are you using v5.3? You will need a version 6. You can get this binary > for v6 here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg > > > On 03/17/2017 11:47 AM, Marissa Pifer wrote: > > > > Marcs-MacBook-Pro:SRMC01-1 marchaut$ mris_apply_reg --src-label > > label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label > > --streg xhemi/surf/lh.fsaverage_sym.sphere.reg > > surf/lh.fsaverage_sym.sphere.reg > > > > ERROR: Option --src-label unknown > > > > > > > > On Fri, Mar 17, 2017 at 11:26 AM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > please send command line > > > > > > On 3/17/17 10:38 AM, Marissa Pifer wrote: > >> Hi freesurfers, > >> > >> I am using xhemi to map the right hemisphere of each subject to > >> the left hemisphere of the same subject. The first xhemi command > >> works fine, but the 2nd step for mapping the label, I get this > >> error: "Option --src-label unknown" > >> > >> Do you know how to fix this? > >> > >> Marissa > >> > >> > >> ___ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > ___ Freesurfer mailing > > list Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <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 > -- > 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] xhemi label
Yes I am using 5.3. Thank you! Marissa On Fri, Mar 17, 2017 at 12:23 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > Are you using v5.3? You will need a version 6. You can get this binary > for v6 here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg > > > On 03/17/2017 11:47 AM, Marissa Pifer wrote: > > > > Marcs-MacBook-Pro:SRMC01-1 marchaut$ mris_apply_reg --src-label > > label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label > > --streg xhemi/surf/lh.fsaverage_sym.sphere.reg > > surf/lh.fsaverage_sym.sphere.reg > > > > ERROR: Option --src-label unknown > > > > > > > > On Fri, Mar 17, 2017 at 11:26 AM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > please send command line > > > > > > On 3/17/17 10:38 AM, Marissa Pifer wrote: > >> Hi freesurfers, > >> > >> I am using xhemi to map the right hemisphere of each subject to > >> the left hemisphere of the same subject. The first xhemi command > >> works fine, but the 2nd step for mapping the label, I get this > >> error: "Option --src-label unknown" > >> > >> Do you know how to fix this? > >> > >> Marissa > >> > >> > >> ___ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > ___ Freesurfer mailing > > list Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <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 > -- > 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] xhemi label
Marcs-MacBook-Pro:SRMC01-1 marchaut$ mris_apply_reg --src-label label/rh.V1_exvivo.thresh.label --trg rh-on-lh.V1_exvivo.thresh.label --streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg ERROR: Option --src-label unknown On Fri, Mar 17, 2017 at 11:26 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > please send command line > > On 3/17/17 10:38 AM, Marissa Pifer wrote: > > Hi freesurfers, > > I am using xhemi to map the right hemisphere of each subject to the left > hemisphere of the same subject. The first xhemi command works fine, but the > 2nd step for mapping the label, I get this error: "Option --src-label > unknown" > > Do you know how to fix this? > > Marissa > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 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] xhemi label
Hi freesurfers, I am using xhemi to map the right hemisphere of each subject to the left hemisphere of the same subject. The first xhemi command works fine, but the 2nd step for mapping the label, I get this error: "Option --src-label unknown" Do you know how to fix this? Marissa ___ 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] Getting combined bvals/bvecs
Hi Anatasia, Thank you for your reply, I'm sorry for responding so later, I have been trying a few different things in order to get tracula to work. I did what you suggested and compiled the bvals and bvecs into one file, in the same order as the images. This got me further, but the trac-all -prep step is still not completing without error. The lastest problem I can't get past is this: "WARNING Multiple image files detected: /users/marchaut/Documents/myprojects/R01/TESTS/TEST1/dmri/dwi.nii /Users/marchaut/Documents/myprojects/R01/TESTS/TEST1/dmri.dwi.nii.gz STOPPING PROGRAM Darwin Marcs-Macbook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016, root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Nov 11 14:46:42 EST 2016" But since I'm combining the AP and PA images files, wouldn't it be necessary for there to be multiple image files? Marissa On Wed, Sep 14, 2016 at 9:54 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Marissa - You have to specify as many b-values and gradient vectors as > there are volumes in your DWI data file. This means that, if you combine > the AP and PA volumes, you also have to concatenate the bvals from the two > into one file, and do the same with the bvecs. Make sure that the order in > which the AP and PA volumes are combined is the same as the order in which > the corresponding bvals and bvecs are combined. > > Hope this helps, > > a.y > > > On Wed, 14 Sep 2016, Marissa Pifer wrote: > > Hello freesurfer experts, >> I am trying to run tracula on subjects that have separate AP/PA direction >> DTI files. We combined the data >> into one using topup, and would now like to run tracula on the subject. >> The problem is, the combined file >> doesn't have a bvals/bvecs file. When I try to use the original bval/bvec >> files, I get the error that the >> bvals and bvecs don't match up. I have tried combining the files into >> one, and then running a dicom to >> nifty conversion to get a combined bvals/bvecs output, but that results >> again in two separate bvals/bvecs >> files as well. I then tried just have two specified bvals and bvecs. This >> did not give us an error >> message, but trac-prep took only a few seconds and did not complete the >> steps it was supposed to to create >> the directories for trac-bedp to complete. I have attached our >> dmrirc.example file and the log for the >> trac-prep step for your reference. >> >> The questions then are; is there a way to get one bvals/bvecs file that >> has the correct parameters for the >> AP and PA combined file. Or, if not, is there a way to run tracula with >> two sets of bvals and bvecs (one >> for the AP and one for the PA direction)? >> >> In case you need this information, the process is being run with >> freesurfer 5.3, on a macbook pro OS X >> version 10.9.5. >> >> Thank you in advance, >> >> Marissa >> >> > ___ > 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 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] How to get numerical r values from analysis
Hi freesurfer experts, I've run into a problem of not being able to generate the numerical results of the analysis I've run through qdec.After I ran the analysis in qdec I opened the overlay in tksurfer, applied a label, and found a significant negative correlation between cortical thickness and one of our variables. I cannot figure out how to get the numerical r value of this correlation. How can I get this value? Thanks in advance Marissa ___ 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 - cannot allocate memory
That fixed the error. Thank you so much for your help! Marissa Pifer On Wed, May 11, 2016 at 11:32 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > Try re-running recon-all -qcache for that subject and see if the error > goes away > > On 05/11/2016 10:56 AM, Marissa Pifer wrote: > > The error was generated on that first subject 03-1, but it was > > successful on all of the other subjects. Is there something wrong with > > that file that we have to exclude that subject from the analysis? > > > > Marissa > > > > On Wed, May 11, 2016 at 10:38 AM, Douglas Greve > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > OK, it is failing on the mri_concat command. It may be that one > > of those inputs is causing the problem. Can you run the command > > with each input separately, eg, > > mri_concat > > > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-1.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh > > --o deleteme.mgh > > mri_concat > > > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-2.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh > > --o deleteme.mgh > > ... > > > > and see if there is one that generates the error > > > > > > > > On 5/11/16 9:15 AM, Marissa Pifer wrote: > >> Here is everything in the terminal after I hit analyze: > >> > >> Data table loading completed successfully. > >> > >> SUBJECTS_DIR is '/Users/marchaut/Documents/myprojects/SOARmaster' > >> > >> lh-Avg-Intercept-thickness --- > >> > >> Does the average thickness differ from zero? > >> > >> 1.000 1.000; > >> > >> > >> lh-Diff-1-2-Intercept-thickness --- > >> > >> Does the average thickness differ between 1 and 2? > >> > >> 1.000 -1.000; > >> > >> > >> ninputs = 28 > >> > >> Checking inputs > >> > >> mri_concat(4256,0x7fff78a00310) malloc: *** > >> mach_vm_map(size=4619122851646017536) failed (error code=3) > >> > >> *** error: can't allocate region > >> > >> *** set a breakpoint in malloc_error_break to debug > >> > >> znzTAGskip: tag=586130367, failed to calloc 2856323072 bytes! > >> > >> > >> Cannot allocate memory > >> > >> Error in Analyze: command failed: mri_concat > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-1.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-2.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR04-1.long.SOAR04/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR04-2.long.SOAR04/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR05-1.long.SOAR05/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR05-2.long.SOAR05/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR06-1.long.SOAR06/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR06-2.long.SOAR06/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR07-1.long.SOAR07/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR07-2.long.SOAR07/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR09-1.long.SOAR09/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR09-2.long.SOAR09/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR17-1.long.SOAR17/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR17-2.long.SOAR17/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR19-1.long.SOAR19/surf/lh.thickness.fwhm10.fsaverage.mgh > >> > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR19-2.long.SOAR19/surf/lh.thickness.fwhm10.fsaverage.mgh > >> &g
Re: [Freesurfer] QDEC - cannot allocate memory
The error was generated on that first subject 03-1, but it was successful on all of the other subjects. Is there something wrong with that file that we have to exclude that subject from the analysis? Marissa On Wed, May 11, 2016 at 10:38 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > OK, it is failing on the mri_concat command. It may be that one of those > inputs is causing the problem. Can you run the command with each input > separately, eg, > mri_concat > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-1.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh > --o deleteme.mgh > mri_concat > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-2.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh > --o deleteme.mgh > ... > > and see if there is one that generates the error > > > > On 5/11/16 9:15 AM, Marissa Pifer wrote: > > Here is everything in the terminal after I hit analyze: > > Data table loading completed successfully. > > SUBJECTS_DIR is '/Users/marchaut/Documents/myprojects/SOARmaster' > > lh-Avg-Intercept-thickness --- > > Does the average thickness differ from zero? > > 1.000 1.000; > > > lh-Diff-1-2-Intercept-thickness --- > > Does the average thickness differ between 1 and 2? > > 1.000 -1.000; > > > ninputs = 28 > > Checking inputs > > mri_concat(4256,0x7fff78a00310) malloc: *** > mach_vm_map(size=4619122851646017536) failed (error code=3) > > *** error: can't allocate region > > *** set a breakpoint in malloc_error_break to debug > > znzTAGskip: tag=586130367, failed to calloc 2856323072 bytes! > > > Cannot allocate memory > > Error in Analyze: command failed: mri_concat > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-1.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-2.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR04-1.long.SOAR04/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR04-2.long.SOAR04/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR05-1.long.SOAR05/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR05-2.long.SOAR05/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR06-1.long.SOAR06/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR06-2.long.SOAR06/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR07-1.long.SOAR07/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR07-2.long.SOAR07/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR09-1.long.SOAR09/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR09-2.long.SOAR09/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR17-1.long.SOAR17/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR17-2.long.SOAR17/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR19-1.long.SOAR19/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR19-2.long.SOAR19/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR23-1.long.SOAR23/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR23-2.long.SOAR23/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1.long.SOAR26/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-2.long.SOAR26/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR27-1.long.SOAR27/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR27-2.long.SOAR27/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR28-1.long.SOAR28/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR28-2.long.SOAR28/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR30-1.long.SOAR30/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR30-2.long.SOAR30/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR31-1.long.SOAR31/surf/lh.thickness.fwhm10.fsaverage.mgh > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR31-2.long.SOAR31/surf/lh.thickness.fwhm10
Re: [Freesurfer] QDEC - cannot allocate memory
Here is everything in the terminal after I hit analyze: Data table loading completed successfully. SUBJECTS_DIR is '/Users/marchaut/Documents/myprojects/SOARmaster' lh-Avg-Intercept-thickness --- Does the average thickness differ from zero? 1.000 1.000; lh-Diff-1-2-Intercept-thickness --- Does the average thickness differ between 1 and 2? 1.000 -1.000; ninputs = 28 Checking inputs mri_concat(4256,0x7fff78a00310) malloc: *** mach_vm_map(size=4619122851646017536) failed (error code=3) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug znzTAGskip: tag=586130367, failed to calloc 2856323072 bytes! Cannot allocate memory Error in Analyze: command failed: mri_concat /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-1.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR03-2.long.SOAR03/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR04-1.long.SOAR04/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR04-2.long.SOAR04/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR05-1.long.SOAR05/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR05-2.long.SOAR05/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR06-1.long.SOAR06/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR06-2.long.SOAR06/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR07-1.long.SOAR07/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR07-2.long.SOAR07/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR09-1.long.SOAR09/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR09-2.long.SOAR09/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR17-1.long.SOAR17/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR17-2.long.SOAR17/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR19-1.long.SOAR19/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR19-2.long.SOAR19/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR23-1.long.SOAR23/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR23-2.long.SOAR23/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1.long.SOAR26/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-2.long.SOAR26/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR27-1.long.SOAR27/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR27-2.long.SOAR27/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR28-1.long.SOAR28/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR28-2.long.SOAR28/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR30-1.long.SOAR30/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR30-2.long.SOAR30/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR31-1.long.SOAR31/surf/lh.thickness.fwhm10.fsaverage.mgh /Users/marchaut/Documents/myprojects/SOARmaster/SOAR31-2.long.SOAR31/surf/lh.thickness.fwhm10.fsaverage.mgh --o /Users/marchaut/Documents/myprojects/SOARmaster/qdec/test1/y.mgh XIO: fatal IO error 35 (Resource temporarily unavailable) on X server "/tmp/launch-NzfFao/org.macosforge.xquartz:0" after 16398 requests (16398 known processed) with 0 events remaining. On Tue, May 10, 2016 at 5:41 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Is that all it says? At one point (about 3-4 years ago) we would see > that error because some of our files got corrupted. Can you send more of > the terminal output? > > On 05/10/2016 12:56 PM, Marissa Pifer wrote: > > Hi freesurfers, > > > > I am on a macbook pro OSX 10.9.5, trying to run an analysis on qdec - > > freesurfer version 5.3. I am looking to analyze T2weighted scans for > > 27 subjects through the qdec system. I keep getting this error that it > > cannot allocate memory for the task. I'v been talking with our IT > > people and they've told me I have more than enough space on the > > computer, so it must be an issue with the program or how it's set up. > > > > This is the error message: > > > > > > *** error: can't allocate
[Freesurfer] QDEC - cannot allocate memory
Hi freesurfers, I am on a macbook pro OSX 10.9.5, trying to run an analysis on qdec - freesurfer version 5.3. I am looking to analyze T2weighted scans for 27 subjects through the qdec system. I keep getting this error that it cannot allocate memory for the task. I'v been talking with our IT people and they've told me I have more than enough space on the computer, so it must be an issue with the program or how it's set up. This is the error message: *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug znzTAGskip: tag=586130367, failed to calloc 2856323072 bytes! Cannot allocate memory Does anyone know what I can do to fix this problem? Thanks, Marissa ___ 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] bvals bvecs Error
Hi freesurfers, I'm having a problem the bvals and bvecs for one of my subject's DTI data. When I try to run the first step of tracula I get this error message: "Error: data and bvals/bvecs do not contain the same number of entries" I have checked, the bvals and bvecs do contain the same amount of entries (42), and they are in the proper format (bvals one line, bvecs three lines). The entries in the bvals/bvecs matches the number of images within the DTI file as well. Looking online, I saw that this was part of the FAQs on tracula. It suggested making sure the locale settings were correct, which it is (en_US.UTF-8). I've run tracula on every other subject and have not run into this problem, but the same subject had an error with multiple frames when we were processing the T2 images. Could this be related? Any idea about what is going on, or how I can fix it? Thanks in advance, Marissa ___ 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] Multiple Frames Error
Absolutely, I've contacted them about it, and if it is not the right one, I can use the other. There are only 2 frames so I can narrow it down at least. Marissa On Mon, Feb 22, 2016 at 3:46 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > But is that the right frame to use? I would check with whoever collected > the data and get it sorted out before diving into an analysis. > > On 02/22/2016 02:34 PM, Marissa Pifer wrote: > > Bruce, > > > > I'm not sure why it has multiple frames. It was a spin echo, T1 > > weighted structural MRI. I input the command you suggested and > > recon-all is running now. > > > > Thank you for your help! > > > > Marissa > > > > On Mon, Feb 22, 2016 at 12:24 PM, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>> wrote: > > > > Hi Marissa > > > > why does it have multiple frames? What kind of acquisition was it? > > If you know which frame is the correct one you can always extract > > it, for example > > > > cd /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig > > mv 001.mgz two_frames.mgz > > mri_convert -nth 0 two_frames.mgz 001.mgz > > > > Bruce > > > > > > On Mon, 22 Feb 2016, Marissa Pifer wrote: > > > > Hi freesurfers, > > I am trying to run the recon-all command on a T1 weighted > > structural image for one of my subjects and I keep getting > > this error > > > > "Checking for (invalid) multi-frame inputs... > > > > ERROR: input(s) cannot have multiple frames! > > > > > /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz > > has 2 frames > > > > Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version > > 13.4.0: Sun Aug 17 19:50:11 PDT 2014; > > root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 > > > > > > recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 > > 11:13:26 EST 2016" > > > > > > I looked through the mailing list and saw that a few other > > people have had this problem as well, and I tried some of the > > solutions that were suggested but still have not been able to > > get past this. I have run the recon-all command on all of the > > other subjects in our data set, and none of them have this > > problem. Not sure what is different about this scan. > > > > > > Anyone run into this problem and were able to fix it? > > > > > > Thanks in advance, > > > > > > Marissa > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu 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 > > -- > 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] Multiple Frames Error
Bruce, I'm not sure why it has multiple frames. It was a spin echo, T1 weighted structural MRI. I input the command you suggested and recon-all is running now. Thank you for your help! Marissa On Mon, Feb 22, 2016 at 12:24 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Marissa > > why does it have multiple frames? What kind of acquisition was it? If you > know which frame is the correct one you can always extract it, for example > > cd /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig > mv 001.mgz two_frames.mgz > mri_convert -nth 0 two_frames.mgz 001.mgz > > Bruce > > > On Mon, 22 Feb 2016, Marissa Pifer wrote: > > Hi freesurfers, >> I am trying to run the recon-all command on a T1 weighted structural >> image for one of my subjects and I keep getting this error >> >> "Checking for (invalid) multi-frame inputs... >> >> ERROR: input(s) cannot have multiple frames! >> >> /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz >> has 2 frames >> >> Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun >> Aug 17 19:50:11 PDT 2014; >> root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 >> >> >> recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016" >> >> >> I looked through the mailing list and saw that a few other people have >> had this problem as well, and I tried some of the >> solutions that were suggested but still have not been able to get past >> this. I have run the recon-all command on all of the >> other subjects in our data set, and none of them have this problem. Not >> sure what is different about this scan. >> >> >> Anyone run into this problem and were able to fix it? >> >> >> Thanks in advance, >> >> >> Marissa >> >> >> > ___ > 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 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] Multiple Frames Error
Hi freesurfers, I am trying to run the recon-all command on a T1 weighted structural image for one of my subjects and I keep getting this error "Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig/001.mgz has 2 frames Darwin Marcs-MacBook-Pro.local 13.4.0 Darwin Kernel Version 13.4.0: Sun Aug 17 19:50:11 PDT 2014; root:xnu-2422.115.4~1/RELEASE_X86_64 x86_64 recon-all -s SOAR26-1 exited with ERRORS at Mon Feb 22 11:13:26 EST 2016" I looked through the mailing list and saw that a few other people have had this problem as well, and I tried some of the solutions that were suggested but still have not been able to get past this. I have run the recon-all command on all of the other subjects in our data set, and none of them have this problem. Not sure what is different about this scan. Anyone run into this problem and were able to fix it? Thanks in advance, Marissa ___ 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 Run Time
Hi Freesurfers, I've recently downloaded free surfer onto a new computer. It's working correctly, but the running time for the recon-all -all command is 30-50 hours. This is in contrast to when I've used free surfer on previous computers where the run time was 6-12 hours. I'm wondering why this would be the case and if anyone else has run into this problem. Marissa ___ 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.
