Freesurfer July 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
160 discussions

Flag(s) for parallel processing
by Billah, Tashrif 17 Jul '20

17 Jul '20

This<https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes> says "-openmp <num> after -parallel", this<https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures> says "export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2", while this<https://surfer.nmr.mgh.harvard.edu/fswiki/mri_coreg> says "--threads nthreads" for parallel processing. I want to run recon-all and want all processes under recon-all to be parallelized. Which one(s) of the above flags should I provide with recon-all? Please note that the values are not my interest, the flags are. I know the proper values I should choose for the flags on my machines. So far I have been trying "-parallel -openmp 4" option only but my run time stays over 5 hours contrary to less than 3 hours stipulated in the documentation. -Tashrif .

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PETSurfer analysis question
by Ferraro, Pilar 16 Jul '20

16 Jul '20

External Email - Use Caution Hi Freesurfer experts, I’ve run a PETSurfer analysis in order to compare mean uptake values of ROIs obtained with different methods: No PVC, SGTM, MG and MZ. However, I’ve now extracted the mean values and they are extremely heterogeneous. As an example, the same ROI (lh banks of the superior temporal sulcus) has the following uptake values: No PVC= 1.709 SGTM= 2.495 MG= 23.847 MZ= 15.564 I’m particularly worried for the huge difference between noPVC - SGTM values and MG-MZ values. Any advice? I wonder whether this finding is normal or there is something I’ve missed. Many thanks, Pilar Il giorno 15 lug 2020, alle ore 6:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> ha scritto: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: recon all Freesurfer 7.1 on Mac High Sierra fails to run for some subjects (Douglas N. Greve) 2. Re: mri_fieldsign error (Douglas N. Greve) 3. Extracting PET Binding Values from Inflated Surface (O'Dell, Ryan) ---------------------------------------------------------------------- Message: 1 Date: Wed, 15 Jul 2020 11:12:21 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra fails to run for some subjects To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <beb084b0-fe6b-c8a2-c0a5-e8bcc92769b6(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" Can you send the recon-all.log file for some of the failures? On 7/15/2020 10:52 AM, Annelies Vant Westeinde wrote: ????????External Email - Use Caution Dear list, As described by others on this list, recon-all with Freesurfer 7.1 on a Mac operating system seems to fail for around 10% of the subjects. The following solution was offered: sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/rca-lon… -o rca-long-tp-init sudo chmod +x rca-long-tp-init However, this did not solve the problem for me. I re-ran recon-all for the same subjects, but it still failed, some of them at the following step: "####################################### GCADIR /Applications/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /Applications/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs #######################################" It simply stopped running there. Others did finish running, but instead got a segmentation fault error. What could I do? I have Mac High Sierra. Annelies Annelies van't Westeinde?| PHD Candidate Department of Women's and Children's Health | Karolinska Institutet 171 77 Solna | Karolinskav?gen 37A +46 760967499 annelies.vant.westeinde(a)ki.se | ki.se <http://ki.se/en/startpage> ______________________________________ Karolinska Institutet ? a medical university /N?r du skickar e-post till Karolinska Institutet (KI) inneb?r detta att KI kommer att behandla dina personuppgifter. /H?r finns information om hur KI behandlar personuppgifter <https://ki.se/medarbetare/integritetsskyddspolicy>. /Sending email to Karolinska Institutet (KI) will result in KI processing your personal data./ You can read more about KI?s processing of personal data here <https://ki.se/en/staff/data-protection-policy>. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200715/0… ------------------------------ Message: 2 Date: Wed, 15 Jul 2020 11:14:53 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] mri_fieldsign error To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <5364c956-1d58-e69d-5635-6fde5dd41c91(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" I don't know what is going wrong here. One simple thing to check is to make sure that all the input files have the same number of vertices as the surface. If that is the case, then upload the subject and input files using the instructions below From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log? into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: use "anonymous" (no quotes) It will ask you for a password: use "anonymous" (no quotes) cd transfer/incoming binary put subject.tar.gz Send an email that the file has been and the name of the file. On 7/15/2020 11:07 AM, Xiaomin Yue wrote: ????????External Email - Use Caution Hi All, Just in case the below poster was missed. Thanks, Xiaomin *From: *Xiaomin Yue <mailto:yuexm@hotmail.com> *Sent: *Saturday, July 11, 2020 1:43 PM *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *[Freesurfer] mri_fieldsign error *????????External Email - Use Caution * Hi Doug, I used FS 7.1 under WSL to analyze retinotopy data.? Since the ring and wedge were presented at a different frequency, the data had to be analyzed separately for each condition.? To get the field sign, I had to use the mri_fieldsign function to combine polar and eccen data. However, an error happened with running mri_fieldsign: ?Segmentation fault????? (core dumped)?.? The following is the command-line output. Thanks for your help! Xiaomin cwd /mnt/d/xyLinuxStaff/projects/wedge_amygdala cmdline mri_fieldsign --fs LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz --polar LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz --eccen ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz --s LOO --hemi rh --sphere sysname? Linux hostname DESKTOP-SVDQE4Q machine? x86_64 user???? xiaominyue eccen real ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/real.nii.gz eccen imag ../ring_amygdala/LOO_xy/bold/rtopy.ring.self.rh/eccen/imag.nii.gz polar real LOO_xy/bold/rtopy.wedge.self.rh/polar/real.nii.gz polar imag LOO_xy/bold/rtopy.wedge.self.rh/polar/imag.nii.gz patch???? (null) subject???? LOO hemi??????? rh fwhm??????? -1.000000 nsmooth???? -1 fieldsign LOO_xy/bold/rtopy.wedge.self.rh/fieldsign/fieldsign.nii.gz usenew????? 1 Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/surf/rh.sphere Using spherical coordinates Reading /mnt/d/xyLinuxStaff/anatMRI_amy//LOO/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Complex Ripping Zeros Rot (rad): 0 0 surfer: compute_fieldsign2() dthresh = 1.5 shape = 1 nvertices = 153801 ??? 0???? 0 45452?? 0.03? 33.2224 1018? 1000 39160? 21.33? -18.3959 2055? 2000 44734? 43.26? 33.0783 3148? 3000 49793? 65.38? 0.653687 4344? 4000 38626? 88.16? 16.7555 5529? 5000 54149 110.12? -4.90118 6706? 6000 61599 133.36? -5.74607 7971? 7000 50134 155.88? -17.5589 9165? 8000 34182 178.05? -18.9387 10591? 9000 59682 200.70? -4.60514 12034 10000 63856 223.18? -4.4884 13297 11000 41007 245.62? 27.3489 14938 12000 27365 267.70? -1.40077 16684 13000 23615 289.10? -0.518007 18048 14000 47088 309.37? 18.7017 19798 15000 21060 330.11? 15.9458 21681 16000 33067 350.27? -11.1953 23173 17000 28744 371.48? -6.18747 25112 18000 27738 392.41? -6.93845 26953 19000 20538 414.47? 2.99349 28903 20000 80583 435.98? -0.338512 30319 21000 16251 459.83? -45.2313 32174 22000 17139 483.36? -2.31642 34093 23000 13307 507.02? 19.1461 36170 24000 17826 530.65? -10.7575 37683 25000 69324 555.78? -6.17011 39666 26000 14043 583.29? -10.5151 41746 27000 76017 609.92? -0.0112556 43986 28000 84646 636.28? 1.24722 46088 29000 9763 664.26? 12.7035 48326 30000 92161 694.30? 2.03416 50431 31000 99884 724.91? 1.20525 ./xy_make_wedge_fieldsign.bash: line 21: 22473 Segmentation fault????? (core dumped) mri_fieldsign --fs $line/bold/rtopy.wedge.self.$hemi/fieldsign/fieldsign.nii.gz --polar $line/bold/rtopy.wedge.self.$hemi/polar/real.nii.gz $line/bold/rtopy.wedge.self.$hemi/polar/imag.nii.gz --eccen ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/real.nii.gz ../ring_amygdala/$line/bold/rtopy.ring.self.$hemi/eccen/imag.nii.gz --s $subjname --hemi $hemi --sphere _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200715/e… ------------------------------ Message: 3 Date: Wed, 15 Jul 2020 15:39:08 +0000 From: "O'Dell, Ryan" <ryan.odell(a)yale.edu> Subject: [Freesurfer] Extracting PET Binding Values from Inflated Surface To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BN8PR08MB5825811A87A2758B0DDC2D25F57E0(a)BN8PR08MB5825.namprd08.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" External Email - Use Caution Hi Doug, I have a question surrounding our attempts to extract PET binding values (BPND/DVR) which have been first transformed into FS subject space, mapped to the cortical surface using mri_vol2surf (signal averaged over the middle 80% of the cortical ribbon), and then displayed on the inflated hemisphere surfaces. We would like to extract the average binding values from the cortical surface ROIs using the Desikan-Killiany atlas, but are unsure how to go about this. Is there a simple way to use aparcstats2table or a similar command to extract average values from surface ROIs as defined by the ?h.aparc.annot file? Thanks! Ryan O'Dell MD/PhD PGY4 Psychiatry Resident, Yale University -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200715/5… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 197, Issue 33 *******************************************

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fMRI paired analysis
by Agnieszka Sabisz 16 Jul '20

16 Jul '20

External Email - Use Caution Dear Freesurfer team! I'm trying to make a statistics of resting state fMRI data in fsfast. I have one group of patients and two timepionts. I read how to perform the paired analysis in structural studies in freesurfer. In structural images the difference between the timepoints should be prepared in mri_preproc command. Should I add the same command --paired-diff to isxconncat? If not, how to perform the paired test? Best regards, Agnieszka

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Cortical Parcellations in FreeSurfer 7
by Al Qadi, Ameen 15 Jul '20

15 Jul '20

External Email - Use Caution Dear Freesurfer Developers, I hope this email finds you all safe and well. I have two questions regarding the new version of freesurfer: - Is there a new CLUT associated with FS7? I tried to use the CLUT labels to extract thalamic subnuclei ROIs, but got empty ROI files. - Given that Freesurfer version 7 contains segmentations not previously generated in recon-all (i.e. hippocampal subfields), is it possible to extract these ROIs using aparc+aseg images generated using previous versions of Freesurfer? Or do we need to repeat the cortical parcellations (i.e. rerun recon-all) using FS7? I’d highly appreciate your time and feedback on this matter. Thank you. Best, Ameen -- Ameen Al Qadi MSBS Candidate Icahn School Of Medicine at Mount Sinai '20 +1-646-500-1521 ameen.alqadi(a)icahn.mssm.edu

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TRACULA preprocessing error
by Jason Silva Rudberg 15 Jul '20

15 Jul '20

External Email - Use Caution Hello, I have been attempting to run TRACULA on the sample practice data using the sample configuration file listed here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula. I am using Free Surfer 6. I receive an error message at the first step of the pre-processing pathway with subjects elmo.2008 and elmo.2012. It looks like it may be getting hung up at the Eddy Correction step. Do you know why this might be happening? Thank you for your help! Jason *This is the configuration file:* # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = $TUTORIAL_DATA/diffusion_tutorial # Subject IDs # set subjlist = ( elmo.2005 \ elmo.2008 \ elmo.2012 ) # Input diffusion DICOMs # If original DICOMs don't exist, these can be in other image format # but then the gradient table and b-value table must be specified (see below) # set dcmroot = $TUTORIAL_DATA/diffusion_tutorial set dcmlist = ( elmo.2005/orig/656000-11-1.dcm \ elmo.2008/orig/97000-000017-000001.dcm \ elmo.2012/orig/MR.1.3.12.2.1107.5.2.32.35006.2012121819455034689828982 ) # Diffusion gradient tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # The tables must have either three columns, where each row is a gradient vector # or three rows, where each column is a gradient vector # There must be as many gradient vectors as volumes in the diffusion data set # Default: Read from DICOM header # set bveclist = ( $TUTORIAL_DATA/diffusion_tutorial/elmo.2005/orig/gradients.txt \ $TUTORIAL_DATA/diffusion_tutorial/elmo.2008/orig/gradients.txt \ $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/orig/gradients.txt ) #set bvecfile = /path/to/bvecs.txt # Diffusion b-value tables (if there is a different one for each scan) # Must be specified if they cannot be read from the DICOM headers # There must be as many b-values as volumes in the diffusion data set # Default: Read from DICOM header # set bvallist = ( $TUTORIAL_DATA/diffusion_tutorial/elmo.2005/orig/bvalues.txt \ $TUTORIAL_DATA/diffusion_tutorial/elmo.2008/orig/bvalues.txt \ $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/orig/bvalues.txt ) #set bvalfile = /path/to/bvals.txt set runlist = (2) set doeddy = 1 set dorotbvecs = 1 set usemaskanat = 1 set thrbet = 0.3 set doregflt = 0 set doregbbr = 1 set doregmni = 1 set doregcvs = 0 #set mnitemp = /path/to/mni/template #set cvstemp = /cvs/template/name #set cvstempdir = /path/to/parent/dir/of/cvstemp set pathlist = ( lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP ) set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) *This is the attempted run:* [jar269@librapet ~]$ trac-all -corr -c /home1/jar269/Elmo2/dmrirc.tutorial INFO: SUBJECTS_DIR is /home1/jar269/Elmo2/diffusion_recons INFO: Diffusion root is /home1/jar269/Elmo2/diffusion_tutorial Actual FREESURFER_HOME /home1/am2359/freesurfer_6 trac-preproc -c /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/scripts/dmrirc.local -log /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/scripts/trac-all.log -cmd /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/scripts/trac-all.cmd #------------------------------------- /home1/am2359/freesurfer_6/bin/trac-preproc #------------------------------------- #@# Image corrections Sun Jul 12 14:27:04 EDT 2020 mri_convert --bvec-voxel /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm... Getting Series No INFO: Found 74 files in /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig INFO: Scanning for Series Number 17 Scanning Directory INFO: found 70 files in series INFO: loading series header info. RunNo = 16 WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm Identification NumarisVer syngo MR B15 ScannerModel TrioTim PatientName CON04_07172008 Date and time StudyDate 20080717 StudyTime 082602.097000 SeriesTime 091538.382000 AcqTime 091309.512500 Acquisition parameters PulseSeq ep_b0#1 Protocol DTI PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 84 InversionTime -1 RepetitionTime 9850 PhEncFOV 237 ReadoutFOV 237 Image information RunNo 16 SeriesNo 17 ImageNo 1 NImageRows 1152 NImageCols 1152 NFrames 70 SliceArraylSize 79 IsMosaic 1 ImgPos 1042.7820 1078.5270 242.5410 VolRes 1.8516 1.8516 1.8500 VolDim 128 128 79 Vc -0.9997 -0.0232 -0.0095 Vr 0.0249 -0.9576 -0.2870 Vs -0.0024 -0.2872 0.9579 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (128 128 79), nframes = 70, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR B15 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 9850, TR = 9850 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.99969 -0.02379 0.00778 -0.14012; 0.02316 0.99706 0.07309 -9.34992; -0.00949 -0.07288 0.99730 -12.79552; 0.00000 0.00000 0.00000 1.00000; FileName /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm Identification NumarisVer syngo MR B15 ScannerModel TrioTim PatientName CON04_07172008 Date and time StudyDate 20080717 StudyTime 082602.097000 SeriesTime 091538.382000 AcqTime 091309.512500 Acquisition parameters PulseSeq ep_b0#1 Protocol DTI PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 84 InversionTime -1 RepetitionTime 9850 PhEncFOV 237 ReadoutFOV 237 Image information RunNo 16 SeriesNo 17 ImageNo 1 NImageRows 1152 NImageCols 1152 NFrames 70 SliceArraylSize 79 IsMosaic 1 ImgPos 118.6930 148.7646 -38.5453 VolRes 1.8516 1.8516 1.8500 VolDim 128 128 79 Vc -0.9997 -0.0232 -0.0095 Vr 0.0249 -0.9576 -0.2870 Vs -0.0024 -0.2872 0.9579 VolCenter 3.0033 11.5602 -3.6840 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = -0.00244356 -0.287158 0.95788 INFO: no Siemens slice order reversal detected (good!). TR=9850.00, TE=84.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999687, -0.0231588, -0.00949289) j_ras = (0.0249093, -0.957603, -0.287012) k_ras = (-0.00244356, -0.287158, 0.95788) writing to /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.voxel_space.bvecs /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs mri_probedicom --i /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/97000-000017-000001.dcm > /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dcminfo.dat cp /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/gradients.txt /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs cp /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/orig/bvalues.txt /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvals mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs.tmp /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvals.tmp /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvals orientLAS /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 6.34232 mri_convert -oni 128 -onj 128 -onk 79 -oid -0.999687 -0.0231588 -0.00949289 -ojd -0.0249093 0.957603 0.287012 -okd -0.00244356 -0.287158 0.95788 -oc 2.95721 13.3333 -3.15258 -rt nearest /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 128 -onj 128 -onk 79 -oid -0.999687 -0.0231588 -0.00949289 -ojd -0.0249093 0.957603 0.287012 -okd -0.00244356 -0.287158 0.95788 -oc 2.95721 13.3333 -3.15258 -rt nearest /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.999687, -0.0231588, -0.00949289) -> (-0.999687, -0.0231588, -0.00949289) normalizing out_j_direction: (-0.0249093, 0.957603, 0.287012) -> (-0.0249093, 0.957603, 0.287012) normalizing out_k_direction: (-0.00244356, -0.287158, 0.95788) -> (-0.00244356, -0.287158, 0.95788) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.nii.gz... TR=9850.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999687, -0.0231588, -0.00949289) j_ras = (0.0249093, -0.957603, -0.287012) k_ras = (-0.00244356, -0.287158, 0.95788) Reslicing using nearest writing to /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz... INFO: found /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvals, copying INFO: found /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig.bvecs, converting to LAS mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.bvecs /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.bvals /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvals eddy_correct /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi_orig_las.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz 0 processing INTEL Image Exception : #63 :: No image files match: INTEL Image Exception : #22 :: Failed to read volume INTEL Error : No image files match: INTEL Failed to read volume INTEL Error : No image files match: INTEL processing MKL Image Exception : #63 :: No image files match: MKL Image Exception : #22 :: Failed to read volume MKL Error : No image files match: MKL Failed to read volume MKL Error : No image files match: MKL processing ERROR: Image Exception : #63 :: No image files match: ERROR: Image Exception : #22 :: Failed to read volume ERROR: Error : No image files match: ERROR: Failed to read volume ERROR: Error : No image files match: ERROR: processing /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: Image Exception : #63 :: No image files match: /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: Image Exception : #22 :: Failed to read volume /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: Error : No image files match: /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: Failed to read volume /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: Error : No image files match: /home1/jar269/fsl/fslpython/envs/fslpython/lib/python3.7/site-packages/numpy/core/../../../../libmkl_core.so: processing undefined Image Exception : #63 :: No image files match: undefined Image Exception : #22 :: Failed to read volume undefined Error : No image files match: undefined Failed to read volume undefined Error : No image files match: undefined processing symbol: Image Exception : #63 :: No image files match: symbol: Image Exception : #22 :: Failed to read volume symbol: Error : No image files match: symbol: Failed to read volume symbol: Error : No image files match: symbol: processing mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. Image Exception : #63 :: No image files match: mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. Image Exception : #22 :: Failed to read volume mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. Error : No image files match: mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. Failed to read volume mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. Error : No image files match: mkl_pds_lp64_pds_sym_indef_bk_fct_slv_c_seq_nrhs_cmplx. processing Intel Image Exception : #63 :: No image files match: Intel Image Exception : #22 :: Failed to read volume Intel Error : No image files match: Intel Failed to read volume Intel Error : No image files match: Intel processing MKL Image Exception : #63 :: No image files match: MKL Image Exception : #22 :: Failed to read volume MKL Error : No image files match: MKL Failed to read volume MKL Error : No image files match: MKL processing FATAL Image Exception : #63 :: No image files match: FATAL Image Exception : #22 :: Failed to read volume FATAL Error : No image files match: FATAL Failed to read volume FATAL Error : No image files match: FATAL processing ERROR: Image Exception : #63 :: No image files match: ERROR: Image Exception : #22 :: Failed to read volume ERROR: Error : No image files match: ERROR: Failed to read volume ERROR: Error : No image files match: ERROR: processing Cannot Image Exception : #63 :: No image files match: Cannot Image Exception : #22 :: Failed to read volume Cannot Error : No image files match: Cannot Failed to read volume Cannot Error : No image files match: Cannot processing load Image Exception : #63 :: No image files match: load Image Exception : #22 :: Failed to read volume load Error : No image files match: load Failed to read volume load Error : No image files match: load processing libmkl_core.so. Image Exception : #63 :: No image files match: libmkl_core.so. Image Exception : #22 :: Failed to read volume libmkl_core.so. Error : No image files match: libmkl_core.so. Failed to read volume libmkl_core.so. Error : No image files match: libmkl_core.so. Image Exception : #63 :: No image files match: INTEL terminate called after throwing an instance of 'std::runtime_error' what(): No image files match: INTEL /home1/jar269/fsl/bin/eddy_correct: line 103: 13578 Aborted (core dumped) fslmerge -t $output $full_list mv -f /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs.norot xfmrot /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.ecclog /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs.norot /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. 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R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. ln -sf /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/data.nii.gz mri_convert --frame 0 1 2 3 4 5 6 7 8 9 /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/lowb.nii.gz mri_convert.bin --frame 0 1 2 3 4 5 6 7 8 9 /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/lowb.nii.gz niiRead(): error opening file /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home1/jar269/Elmo2/diffusion_tutorial/elmo.2008/dmri/dwi.nii.gz... Linux librapet.med.yale.edu 3.10.0-693.5.2.el7.x86_64 #1 SMP Fri Oct 20 20:32:50 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Sun Jul 12 14:29:05 EDT 2020

2 1

Freesurfer Hippocampal Subfield Misalignment
by Jenna Katherine Blujus 15 Jul '20

15 Jul '20

External Email - Use Caution Hi Experts, I ran the hippocampal subfield segmentation protocol using a T2 image that does not cover the whole brain in Freesurfer v6.0. I noticed that the alignment of the ?h.hippoSfLabels-T2.v10 output to the anatomical boundaries of the hippocampus in some of my subjects is off. For example, the left hippocampal subfield segmentation in one subject is superior and medial to the hippocampus. I checked the aseg.presurf file (since I am using v6.0) and indeed the whole left hippocampus is off. I saw in a previous thread (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23942.html) that it was suggested to edit the hippocampal segmentation within the aseg file to potentially improve alignment of the subfield segmentation. However, a more recent post (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg54543.html) stated that both the wmparc.mgz and aseg.mgz files would need to be edited and that this was not recommended. Do you have any recommendations on how to move forward? I did edit the hippocampal segmentation within the aseg.presurf file in one of my subjects and reran the subfield segmentation command which substantially improved the output (i.e., it overlays on the hippocampus after correction). Would you suggest that I continue with editing the aseg using previously published protocols on segmenting the hippocampus by hand or would you recommend something else? Thanks in advance! Jenna

2 9

issue with voxel-wise map after multiple comparisons
by miracle ozzoude 15 Jul '20

15 Jul '20

External Email - Use Caution Hello Experts, I ran a surface based pet analysis and I found 6 surviving clusters in the cluster-wise map. However, when I tried to view the voxel-wise map ( mc-z.abs.13.sig.voxel.mgh), it displayed as yellow meaning there was nothing (see attached). Shouldn't it be showing regions that survived at voxel-wise level? Any ideas why it isn't displaying the appropriate figure? Also, what does the content of this file (mc-z.abs.13.sig.voxel.max.dat) mean? Thank you. Best, Paul [image: image.png]

2 4

Re: [Freesurfer] Label on fsaverage failure
by Eleni Nikalexi 15 Jul '20

15 Jul '20

External Email - Use Caution Dear Douglas and Bruce,on the same subject, I wanted to ask two questions:1. since the ROIs were obtained on 2mm voxels, is the command $ mri_vol2surf --mov ROI_set1/LeftAngG.img --regheader MNI_1mm --interp nearest --hemi lh --out Left_AngG_tmpfs.mgh --projdist-max 0 1 0.1 --noreshape --trgsubject fsaverage correct, or should I run it on the MNI152 2mm? 2. how can I create afterwards labels for reconned subjects of 1mm voxel size? I already tried the $ mri_vol2label --i Left_AngG_tmpfs.mgh --id 1 --l LeftAngG_tmp.label --surf fsaverage lh white but permission was denied, so then I tried to use tksurfer, but I got an error message:"surfer: Interpreting overlay volume /project/RDS-FHS-ppa2018-RW/eleni/localizers/Left_AngG_tmpfs.mgh as encoded scalar volume". What would you suggest? Thank you in advance!Eleni On Monday, July 6, 2020, 09:29:19 PM GMT+3, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote: It has to be loaded as an overlay to a surface, not a surface itself. On 7/3/2020 10:10 AM, Eleni Nikalexi wrote: External Email - Use Caution Dear Douglas, thank you very much for your help; I run the recon of MNI152_T1_1mm_brain.nii.gz (which I moved into a directory called MNI_1mm). Then I run the following command, as you suggested: $ mri_vol2surf --mov ROI_set1/LeftAngG.img --regheader MNI_1mm --interp nearest --hemi lh --out LeftAngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape But then, in freeview I get the following result: I also get an error when I try to load it as a surface: "LeftAngG_tmp.mgh' has 0 vertices! Probably trying to use a scalar data file as a surface!" What could be the mistake? Best regards, Eleni On Thursday, July 2, 2020, 04:25:54 PM GMT+3, Douglas N. Greve <dgreve(a)mgh.harvard.edu> wrote: Try running recon-all on the MNI152. Load the ROI onto the reconned MNI152; load the surfaces as well and make sure that the ROI intersects with the surface, then use #3 below with --regheader MNI152 instead of --reg tmp.dat. You can also specify --trgsubject fsaverage and mri_vol2surf will map the ROI all the way onto the fsaverage surface On 7/1/2020 10:03 AM, Eleni Nikalexi wrote: External Email - Use Caution Dear Freesurfer developers, We have a series of MRI scans and we are trying to extract cortical thickness in certain regions of interest. The ROIs already exist - some are in .img and some in NIFTI format - and we want to tranform them into labels and then register them on fsaverage. The problem is that the ROIs are in MNI152 space (from SPM), with voxel size=2mm. We have tried various commands to register one of the .img ROIs on fsaverage, but they all failed: - $ fslregister --s fsaverage --mov ROI_set1/LeftAnGG.img --reg tmp.dat - $ tkmedit fsaverage T1.mgz -overlay ROI_set1/LeftAngG.img -overlay-reg tmp.dat - $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --projdist-max 0 1 0.1 --noreshape - $ mri_vol2surf --mov ROI_set1/LeftAngG.img --reg tmp.dat --interp nearest --hemi lh --out Left_AngG_tmp.mgh --targ $SUBJECTS_DIR/fsaverage/mri/orig.mgz The result is that the ROI is either not in the right place, or the right size or we just end up with a weird 3D cross shape in freeview. Could you please suggest something that we could do to fix this? Thank you so much in advance! Best regards, Eleni _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

Error with write_annotation program !
by Martin Juneja 15 Jul '20

15 Jul '20

External Email - Use Caution Hi FreeSurfer experts, I am trying to run write_annonation program in MATLAB and getting following error: >> [v, L, ct] = read_annotation('lh.Yeo2011_7Networks_N1000.annot'); >> ct.table(1:6,1:3) = 1; >> write_annotation('lh_Yeo2011_DMN',v,L,ct); Error using fwrite Invalid file identifier. Use fopen to generate a valid file identifier. Error in write_annotation (line 55) count = fwrite(fp, int32(length(label)), 'int'); I would really appreciate any help in resolving this issue. Thanks !

3 2

mri_aparc2aseg with flag --a2005s
by Anja Samardzija 15 Jul '20

15 Jul '20

External Email - Use Caution Hello, I am trying to run mri_aparc2aseg with the flag --a2005s on a subject that I previously ran recon-all --all on. When trying to run mri_aparc2aseg with --a2005s I get the following error: could not read annot file 010/label/lh.aparc.a2005s.annot No such file or directory ERROR: MRISreadAnnotation() failed 010/label/lh.aparc.a2005s.annot. How do I solve this issue (get the lh.aparc.a2005s.annot file)? Thank you, Anja

2 8

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Freesurfer July 2020