Freesurfer April 2020

freesurfer@nmr.mgh.harvard.edu

101 participants
170 discussions

bbregister & mri_convert
by Octavian Lie 30 Apr '20

30 Apr '20

External Email - Use Caution Dear All, I have seen bbregister command lines using --o option to get the final output (say a .nii vol), and others where bbregister is used to get an lta transform, which is used in a follow-up step (mri_convert with -ns 1 (no scale), and -rl orig.mgz (reslice-like) Are these options equivalent? meaning when using bbregister with '--o x.nii' option, is the output volume x.nii resliced to orig.mgz, and without rescale? Thanks, Octavian

2 2

recon-all
by jiahui 30 Apr '20

30 Apr '20

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute gray matter volume, but for some of my subjects I get the following error when I run the recon-all -all command: ERROR: inflating to sphere (rms error < 2.00) final distance error I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: ubuntu 16.04.6 LTS 3) recon-all.log and figure2020042908160: see attached

2 1

Quick question on tkregister
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 29 Apr '20

29 Apr '20

?Hi all, I'm a little confused about what the most latest GUI software to fix the talairach is at the moment. This page refers to: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview? but the software, tkregister2 seems to be unavailable. Has it been deprecated by tkregister2_cmdl or tkregisterfv? If so what is the command to open up the GUI with FS6? Thanks, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

3 4

Questions about pial_lgi
by 肖伏龙 29 Apr '20

29 Apr '20

External Email - Use Caution hello everyone I have a question about statistics on LGI. for the LGI data, named as lh.pial_lgi, I used mris_preproc as following: mris_preproc --fsgd fsgd.fsgd --cache-in pial_lgi --target fsaverage --hemi lh --out lh.pial_lgi but freesurfer said ERROR: format for lh.pial_lgi not recognized so is there any method to solve this problem? Thank you

3 3

recon-all
by jiahui 29 Apr '20

29 Apr '20

2 1

mri_label2vol
by Mason Wells 29 Apr '20

29 Apr '20

External Email - Use Caution Hi Experts, I want to take an ROI label that I have drawn on the surface and transform this into the volume. I have drawn the label in the T1 anatomical space and I want to keep the label in this space during the conversion. I am currently using this command based off previous forum posts. mri_label2vol --subject S1 --label S1/prf/mid_contra.label --temp S1/mri/orig.mgz --proj frac 0 1 .1 --fillthresh .3 --hemi lh --o S1/prf/contra.nii.gz –identity Can someone let me know if I am on the right track as when I view this volume in FSLeyes, It doesn’t quite look right. If not, any advice would be greatly appreciated. Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

2 1

Longitudinal Hippocampal Subfields Module, existed with errors
by Zeng, Qi 29 Apr '20

29 Apr '20

External Email - Use Caution Hi, I am trying to use the longitudinal pipeline of the “hippocampal subfields and nuclei of amygdala”. Keep getting error messages when running it longitudinal but with no error message running it cross-sectional. I want to know if there is any way to fix the error and to run a longitudinal pipeline successfully. I am using Freesurfer/dev and matlab_runtime/2014b. I got two timepoints for each subject and finished recon-all longitudinal with no errors. 1) First Try segmentHA_T1_long.sh SUBJ_base >> run for about 15 mins and exited with error message: “Error using kvlGEMSMatlab /autofs/space/panamint_005/users/iglesias/software/freesurfer/GEMS2/kvlAtlasMeshDeformationOptimizer.cxx:327: itk::ERROR: AtlasMeshDeformationLBFGSOptimizer(0x2ac1fead7740): search direction is not a descent direction! Error in kvlStepOptimizer (line 11) Error in SegmentSubfieldsT1Longitudinal” >> no mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21 generated. 2) Second Try segmentHA_T1.sh SUBJ1_timepoint1.long.SUBJ1_base segmentHA_T1.sh SUBJ1_timepoint2.long.SUBJ1_base >> run for about 16 mins, most successful but a few with errors: “Error in segmentSubjectT1_autoEstimateAlveusML (line 1539)” Or >> “Open file failed because file '/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m' has invalid content. Details: 'file is closed.failbit is set.' The file "/tmp/MCR_2841219388/.mcrCache8.4/segmen0/autofs/space/panamint_005/users/iglesias/software/freesurfer.GEMS2.terrier/bin/kvlSetMeshCollectionPositions.m" cannot be executed. Error in segmentSubjectT1_autoEstimateAlveusML (line 538)” >> successful done subject or hemisphere generated mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21. 3) Third Try cross-sectional segmentHA_T1.sh SUBJ1_timepoint1 segmentHA_T1.sh SUBJ1_timepoint2 >> run for about 15 mins, all successful with no errors: >> all subjects have mri/lh.amygNucVolumes-T1.v21 and mri/lh.hippoSfVolumes-T1.v21 generated. Manual inspection with freeview, it seems fine with all successful longitudinal and cross sectional subfield segmentation outputs mgz. I wonder if I can fix first try and second try errors so that longitudinal output can be generated. Thank you for your help! Best, Qi -- Ph.D. candidate Icahn School of Medicine at Mount Sinai

2 1

midbrain segmentation does not cover the whole area
by Safi Ullah . 29 Apr '20

29 Apr '20

External Email - Use Caution Dear Freesurfers I segmented the given example subject 'bert' by using the command (following the steps https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures) Step-1: recon-all -all -s bert -brainstem-structures Step-2: recon-all -s bert -brainstem-structures Step-3_a: mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.mgz --id 173 --l midbrain_vt.label Step-3_b: mri_vol2label --c $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.FSvoxelSpacemgz --id 173 --l midbrain_vx.label Now when i view the label file along with the respective segmented volumes, the results i get for both the vertex domain and voxel domain, does not cover the whole midbrain. as shown below. freeview -l midbrain_vt.label -v $SUBJECTS_DIR/bert/mri/nu.mgz -v $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.mgz:colormap=lut [image: image.png] freeview -l midbrain_vx.label -v $SUBJECTS_DIR/bert/mri/nu.mgz -v $SUBJECTS_DIR/bert/mri/brainstemSsLabels.v10.FSvoxelSpace.mgz:colormap=lut [image: image.png] Question No.1. Please let me know, what is wrong with my steps? Question No.2. Please let me know is it possible to generate label files in voxal space but with better resolution? like vertex space. Warm Regards, Safi

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Re: [Freesurfer] convert MNI152 coordinates into vertex index
by Marina Fernández 29 Apr '20

29 Apr '20

External Email - Use Caution Hi Bruce, Thank you very much for the information. It is very useful. I'm taking a look at both possibilities. Regarding the second option you gave me: you can just run through the list of vertices and find the one that is > closest to your MNI coord What file should I use to find the coordinates correspondence? Should I use [l/r].pial? Or maybe [l/r].orig? Do you think it is a good idea to load that file in matlab and look for the closest coordinates there, and see what vertex index those coordinates correspond to? Thank you in advance. Best wishes, Marina

3 2

PVC alternatives in PetSurfer
by Ferraro, Pilar 29 Apr '20

29 Apr '20

External Email - Use Caution Hi Freesurfer experts, I’m trying to test different PVC methods using PetSurfer, and I would much appreciate your advice on the following topic. Running the command: mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o gtmpvc.output The --mgx option should run the Muller-Gartner analysis, with 01 being the GM threshold. What if we would like to run the Meltzer method instead? With which option should we replace the —mgx one? Many thanks for any help, Pilar Il giorno 27 apr 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: Intensity inhomogeneity messing with the wm.mgz (Bruce Fischl) 2. Re: exporting segmented mgz file (Bruce Fischl) 3. Re: Infant freesurfer (COLLEEN PLETCHER) 4. Threshold values changed/modified before display. (Devavrat Vartak PhD) 5. Re: Threshold values changed/modified before display. (Bruce Fischl) 6. Re: [External] Re: Intensity inhomogeneity messing with the wm.mgz (Zeng, Victor (BIDMC - Keshavan - Psychiatry)) 7. Re: [External] Re: Intensity inhomogeneity messing with the wm.mgz (Bruce Fischl) 8. correcting fsaverage surface area by eICV (Paul) 9. Re: Tracula error: ERROR: Must specify input table of gradient vectors (Figueiro Longo, Maria Gabriela) 10. Re: Overlapping Treatments and fsgd files (Douglas N. Greve) 11. Dear professor (???) 12. Re: Contrast file to be used in mri_glimfit (Douglas N. Greve) 13. Re: Mri_segstats for PET data: Reviewer question (Douglas N. Greve) 14. Re: Freeview surface loading error : MRISread failed (Douglas N. Greve) 15. Re: How is Total cortical gray matter volume calculated (Douglas N. Greve) 16. Re: correcting fsaverage surface area by eICV (Douglas N. Greve) 17. Re: Dear professor (Douglas N. Greve) 18. ???????? (???) 19. Re: Tracula error: ERROR: Must specify input table of gradient vectors (Yendiki, Anastasia) ---------------------------------------------------------------------- Message: 1 Date: Sun, 26 Apr 2020 12:03:06 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.2004261157500.6647(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Victor the best way to remove intensity inhomogeneities is with control points usually. The wm.mgz gives us an initial estimate of the surface locations, but we then deform it based on the intensities in the brain.mgz volume. So if it looks like wm extends that far out in the brain your wm.mgz edits are unliekly to fix things cheers Bruce On Sun, 26 Apr 2020, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: Hi Freesurfer developers, I have a subsample of a FS dataset that have scanner-originated hyperintensities in the bilateral supramarginal/temporal lobes. I've manually removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable to recognize these edits when looking at the ?h.white and aparc+aseg.mgz. Is there a possible way to rectify these errors?? I am using FS6 for linux Here are some pictures:? [IMAGE]?[IMAGE] Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________________________________________________________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you. ------------------------------ Message: 2 Date: Sun, 26 Apr 2020 12:04:36 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] exporting segmented mgz file To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.2004261203210.6647(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Atira what was your mri_convert command line? Make sure to specify no scaling of the intensity volume. Can you try adding: -ns 1 to the mri_convert command line, and if that doesn't work send us the full command line and full screen output from it? This is always a good thing to do as it gives us enough information to help cheers Bruce On Sun, 26 Apr 2020, atira gan-zvi bick wrote: ????????External Email - Use Caution???????? Hi I'm new to freesurfer. I used freesurfer to preform Thalamus segmentation, and can see the segmented?volume in freeview. I would like to export?the segmented volume to nii to continue analysis in MRvista. I was able to do this using?mri_convert - however the values in the nifti are not those on the label list (as seen in ?freeview). The number of different values is similar but not the same, and the values themselves? are totally different?(8103-8233 in freeview, 16384 - 32767). It is possible to compare regions based on visual inspection - however that is tedious?and might lead to mistakes. How can I export the labels of each region in the segmented mgz? Any suggestions? I'd appreciate?to learn fro your experience Thanks Atira -- ?"? ????? ??-??? ??? ????? ?????? ???????? ???? ???-??? ??????????? ?????? Atira Bick (Phd) fMRI unit Hadassah medical center, Hebrew University Jerusalem ------------------------------ Message: 3 Date: Sun, 26 Apr 2020 15:57:57 +0000 From: COLLEEN PLETCHER <ccpletcher(a)medicine.wisc.edu> Subject: Re: [Freesurfer] Infant freesurfer To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <6E02A4C7-7B9E-4929-9CD4-DEDB93A40E64(a)medicine.wisc.edu> Content-Type: text/plain; charset="utf-8" External Email - Use Caution That would be great, thank you! Colleen Pletcher colleen(a)tpck.net On Apr 24, 2020, at 3:58 PM, Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> wrote: ? No, but I can definitely keep you in the loop. Lilla On Wed, 22 Apr 2020, COLLEEN PLETCHER wrote: Great, thank you! Do you have any idea around when that feature will be added? Thanks again _________________________________________________________________________________________________________________________________________________________________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> Sent: Wednesday, April 22, 2020 3:02 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Infant freesurfer Yes, I would like to add it. Lilla On Wed, 22 Apr 2020, COLLEEN PLETCHER wrote: Ok, thank you! Do you think this option will eventually be added? ________________________________________________________________________________________________________________________________________________________________________________________________ _ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> Sent: Wednesday, April 22, 2020 2:26 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Infant freesurfer Hi Colleen, The manual editing option has not yet been added to the pipeline. Best, Lilla On Wed, 22 Apr 2020, COLLEEN PLETCHER wrote: Hello. I am working with the infant Freesurfer pipeline. I have noticed that some of our subjects may need to be manually edited, and then run through the pipeline again. However, when I try to do an infant_recon_all command combined with something like autorecon2-wm, I am getting an error that says the command cannot be found. Are there any commands specific to infant Freesurfer that can be used in combination with manual edits? Thanks! _______________________________________________ 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 ------------------------------ Message: 4 Date: Sun, 26 Apr 2020 15:32:25 -0700 From: Devavrat Vartak PhD <dvartak(a)berkeley.edu> Subject: [Freesurfer] Threshold values changed/modified before display. To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CANfw89fO7JtmzL8TJ4cT1UW6seh3OPKBqJasNq0uuBz1sPj3Sg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi freesurfer developers!, I am using Freesurfer 6.0 and the latest (freeview -beta) to display overlays on my flat surfaces. I am a novice user of freesurfer and I am a bit confused with how the overlays are displayed / thresholds calculated. My overlay of rsquare values ranges from 0.2 to 1.0 (i.e all are positive values.). When the overlay is loaded, the threshold histogram depicts values that are negative and positive (centered around zero). 1) Does freeview recaluate/modify the values before they are displayed? 2) Is it possible to display the values of the overlay as they are? Thank you. Stay healthy and safe! Best, Devavrat -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200426/1… ------------------------------ Message: 5 Date: Sun, 26 Apr 2020 18:43:29 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Threshold values changed/modified before display. To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.2004261843030.6647(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Devavrat freeview definitely does not modify the values in any volumes you load for display. cheers Bruce On Sun, 26 Apr 2020, Devavrat Vartak PhD wrote: ????????External Email - Use Caution???????? Hi freesurfer developers!, I am using Freesurfer?6.0 and the latest (freeview? -beta) to display overlays on my flat surfaces. I am a novice user of freesurfer and I am a bit confused with how the overlays are displayed / thresholds calculated. My overlay of rsquare?values ranges from 0.2 to 1.0 (i.e all are positive values.). When the overlay is loaded, the threshold histogram depicts values that are negative and positive (centered around zero). 1) Does freeview recaluate/modify the values before they are displayed? 2) Is it possible to display the values of the overlay as they are??? Thank you. Stay healthy and safe! Best, Devavrat ------------------------------ Message: 6 Date: Sun, 26 Apr 2020 23:28:39 +0000 From: "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" <vzeng(a)bidmc.harvard.edu> Subject: Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <1587943718956.58079(a)bidmc.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi, Thanks for the clarification. From my understanding, control points are used to grab regions that should be white matter, rather than remove regions that aren't white matter. Are there any resources on how you would use control points to remove intensity inhomogeneity? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: Sunday, April 26, 2020 12:03 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz Hi Victor the best way to remove intensity inhomogeneities is with control points usually. The wm.mgz gives us an initial estimate of the surface locations, but we then deform it based on the intensities in the brain.mgz volume. So if it looks like wm extends that far out in the brain your wm.mgz edits are unliekly to fix things cheers Bruce On Sun, 26 Apr 2020, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: Hi Freesurfer developers, I have a subsample of a FS dataset that have scanner-originated hyperintensities in the bilateral supramarginal/temporal lobes. I've manually removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable to recognize these edits when looking at the ?h.white and aparc+aseg.mgz. Is there a possible way to rectify these errors? I am using FS6 for linux Here are some pictures: [IMAGE]?[IMAGE] Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________________________________________________________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you. ------------------------------ Message: 7 Date: Sun, 26 Apr 2020 19:31:53 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.20.2004261930480.6647(a)gate.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Victor control points are used whenever the white matter intensity is incorrect (>>110 or <<110). If you have regions of white matter that are too bright you should be able to put contgrol points in them to bring the region down. For example, if the gm is so bright that it looks like wm, then the nearby white matter should be even brighter cheers Bruce On Sun, 26 Apr 2020, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: Hi, Thanks for the clarification. From my understanding, control points are used to grab regions that should be white matter, rather than remove regions that aren't white matter. Are there any resources on how you would use control points to remove intensity inhomogeneity? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Sent: Sunday, April 26, 2020 12:03 PM To: Freesurfer support list Subject: [External] Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz Hi Victor the best way to remove intensity inhomogeneities is with control points usually. The wm.mgz gives us an initial estimate of the surface locations, but we then deform it based on the intensities in the brain.mgz volume. So if it looks like wm extends that far out in the brain your wm.mgz edits are unliekly to fix things cheers Bruce On Sun, 26 Apr 2020, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote: Hi Freesurfer developers, I have a subsample of a FS dataset that have scanner-originated hyperintensities in the bilateral supramarginal/temporal lobes. I've manually removed these hyperintensities by editing the wm.mgz, yet FS seems to be unable to recognize these edits when looking at the ?h.white and aparc+aseg.mgz. Is there a possible way to rectify these errors? I am using FS6 for linux Here are some pictures: [IMAGE]?[IMAGE] Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________________________________________________________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 8 Date: Mon, 27 Apr 2020 08:15:45 +0200 From: Paul <freesurferlist(a)gmx.com> Subject: [Freesurfer] correcting fsaverage surface area by eICV To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <trinity-5d777bd5-eae6-4a0b-8e07-75552a04faf6-1587968145560@3c-app-mailcom-bs01> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200427/2… ------------------------------ Message: 9 Date: Mon, 27 Apr 2020 13:49:35 +0000 From: "Figueiro Longo, Maria Gabriela" <MFIGUEIROLONGO(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MN2PR04MB71356CD2F7B0BEFCF05A34CF92AF0(a)MN2PR04MB7135.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi, I have been trying different ways to troubleshooting this error without success. I am pasting here the whole error when I try to run "trac-all -prep -c" in the Dev version: INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon INFO: Diffusion root is /autofs/cluster/guptagp/gabi/tracula/Output Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/dev INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864 trac-preproc -c /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/dmrirc.local -log /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.log -cmd /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.cmd ; trac-preproc -c /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/dmrirc.local -log /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.log -cmd /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.cmd ; #------------------------------------- /usr/local/freesurfer/dev/bin/trac-preproc #------------------------------------- #@# Image corrections Mon Apr 27 09:37:59 EDT 2020 mri_convert --bvec-voxel /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz mri_convert --bvec-voxel /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz reading from /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010... Getting Series No INFO: Found 5211 files in /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715 INFO: Scanning for Series Number 102 Scanning Directory INFO: found 140 files in series INFO: loading series header info. RunNo = 101 INFO: sorting. sdfiSameSlicePos() eps = 0.000001 WARNING: file /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ... INFO: (256 256 140), nframes = 1, ismosaic=0 sdfi->UseSliceScaleFactor 0 INFO: rescale not needed datatype = 4, short=4, float=3 PE Dir ROW ROW FileName /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName 3LT050_s1_170715 Date and time StudyDate 20170715 StudyTime 092536.870000 SeriesTime 100956.320000 AcqTime 093429.902500 Acquisition parameters PulseSeq tfl_me3d4_16ns Protocol T1 PhEncDir ROW EchoNo 1 FlipAngle 7 EchoTime 1.69 InversionTime 1100 RepetitionTime 2530 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 101 SeriesNo 102 ImageNo 139 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 54.1349 92.6115 176.0819 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 140 Vc 0.0934 -0.9338 -0.3453 Vr 0.0226 0.3487 -0.9370 Vs 0.4326 0.3520 -0.8301 VolCenter 99.2585 42.3521 -46.1506 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 INFO: no Siemens slice order reversal detected (good!). TR=2530.00, TE=1.69, TI=1100.00, flip angle=7.00 i_ras = (0.0933703, -0.933839, -0.345291) j_ras = (0.0225973, 0.348705, -0.93696) k_ras = (0.432568, 0.35197, -0.830061) writing to /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz... mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat ERROR: Must specify input table of gradient vectors Linux deqi.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Apr 27 09:39:14 EDT 2020 #------------------------------------- /usr/local/freesurfer/dev/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Mon Apr 27 09:39:14 EDT 2020 cp /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat\u2019: No such file or directory cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat\u2019: No such file or directory Linux deqi.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Apr 27 09:39:14 EDT 2020 [deqi:Scripts] (nmr-dev-env) mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat [deqi:Scripts] (nmr-dev-env) mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat [deqi:Scripts] (nmr-dev-env) autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat: Command not found. [deqi:Scripts] (nmr-dev-env) cp autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms cp: cannot stat \u2018autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat\u2019: No such file or directory cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat\u2019: No such file or directory Thanks for the help, Gabriela ________________________________ From: Figueiro Longo, Maria Gabriela Sent: Friday, April 24, 2020 10:47 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Tracula error: ERROR: Must specify input table of gradient vectors Hello Dear Freesurfer Developers, I am attempting to run Tracula in the last to subject of my study (I had processed all the other subjects using the same script without problems). However, when I try to run the scrip bellow, I am having the error: " ERROR: Must specify input table of gradient vectors " I am reviewed the associated DICOM images and couldn't find any problem with the images. I reviewed a couple emails in the list, but couldn't find a clear reason for keeping having this error. I am using the Freesurfer Dev version. I really appreciate any help. Thank you, Gabriela # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output # Subject IDs (one per time point per subject) # set subjlist = ( 3LT050_s1_170715 ) # Longitudinal base template subject IDs (one for each time point above) # set baselist = ( 3LT050 ) # In case you want to analyze only Huey and Louie # Default: Run analysis on all time points and subjects # # set runlist = (1 2 5 6) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data set dcmlist = ( 3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.20170715092715598296003 ) Gabriela Longo, MD, MSc. Emergency Radiology Clinical Fellow, Emergency Radiology Division Massachusetts General Hospital (MGH) mfigueirolongo(a)mgh.harvard.edu Phone: +1 857 214 0568 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200427/5… ------------------------------ Message: 10 Date: Mon, 27 Apr 2020 11:00:33 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Overlapping Treatments and fsgd files To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <be280c60-71d0-f32e-b3d5-69b2f2a8b55d(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Hi Matt, the 2nd configuration is correct (the one with 8 classes). It looks like your contrast matrix is correct too. The design matrix and contrast matrix are set up for DOSS, which is probably ok too. doug On 4/23/2020 12:17 PM, Matthew Peverill wrote: ????????External Email - Use Caution Hello all, I hope everyone is staying safe and sane out there. I'm running an analysis looking at brain structure differences associated with two separate environmental exposures in children (both dichotomous variables). I am controlling for sex and age, and I'm not interested in interaction effects. My go-to strategy does not match the documentation, but I'm not sure the documented solution using fsgd files will meet my needs. I was hoping I could check with the list about best practices. Because some participants have both exposures, my intuition was to use dummy coded variables so that the design matrix looks like this: +1.00000 +3.11124 -0.48322 -0.51007 -0.53020 +1.00000 -0.20820 +0.51678 -0.51007 -0.53020 +1.00000 -2.06654 -0.48322 -0.51007 -0.53020 ... Where the columns are (mean, mean centered age, mean centered sex, mean centered exposure 1, mean centered exposure 2). A contrast for exposure 1 - exposure 2 would then look like this: [0, 0, 0, 1, -1] However, it's clear from the documentation that, given 3, 2 level factors, the recommended approach is to specify 8 classes (one for every combination of factors) and the covariate in an fsgd file. I can remove the interaction terms from the resulting matrix, but even so it looks very different than what I had above: +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +3.11124 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 -2.06654 ... With a contrast with all classes with exposure 1 set to '1', and all classes with exposure 2 set to '-1' - with the order of the classes in the fsgd file it comes out as [-1 -1 1 1 1 1 -1 -1 0]. I'm not positive that this is the right way to model differences associated with each exposure given unequal #s of participants with neither/both/just one exposure, but I certainly don't have?the expertise to be certain. Could someone give me some guidance on the best approach here? Thank you, ? ? -Matt -- Matthew Peverill 857-277-9083 mrpeverill(a)gmail.com <mailto:mrpeverill@gmail.com> (preferred) pronouns: he/his _______________________________________________ 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/20200427/e… ------------------------------ Message: 11 Date: Mon, 27 Apr 2020 23:05:44 +0800 (CST) From: ??? <xiaofulong1681(a)163.com> Subject: [Freesurfer] Dear professor To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <323d0afc.a015.171bc2c310d.Coremail.xiaofulong1681(a)163.com> Content-Type: text/plain; charset="gbk" External Email - Use Caution Dear professor: I have a question to consult you. I have used the software CAT loaded in matlab to calculate the local gyrification index (LGI) and obtain a .gii file. But I want to use DODS model in freesurfer to statistics the LGI, so now I have to convert the .gii file into .mgh file. I have tried the mris_convert in freesurfer to carry out this but it seemed failed, so would you kind to show or tell me how to convert the .gii file to .mgh file? Thank you very much! I am looking forwards to hear from you. Sincerely, Fulong Xiao -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200427/8… ------------------------------ Message: 12 Date: Mon, 27 Apr 2020 11:06:43 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Contrast file to be used in mri_glimfit To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <5d1343c3-f806-5214-55a0-4055719148d0(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" It looks like you have defined a class in the header, but there is no subject assigned to that class. This causes an erropr On 4/24/2020 1:46 AM, Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience wrote: ????????External Email - Use Caution I tried running mri_glmfit and this error is occurring - WARNING: gdfReadV1: class B,,,,, is defined but not used. INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 ,,,Gender,Age,AQ_Top_Quart nan nan Class Means of each Continuous Variable 1 B,,,,,nan 2 NB,,,,,nan INFO: gd2mtx_method is dods Reading source surface /Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/surf/lh.?-glmdir MRISread(/Applications/freesurfer/BAP/group_analysis_data/qdec/fsaverage/surf This is probably?related to some error in my .mtx file. Thank you, Alex Job On Fri, Apr 24, 2020 at 12:31 AM Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience <ladn(a)email.gwu.edu <mailto:ladn@email.gwu.edu>> wrote: Dear?Freesurfer experts, I am a little bit confused on how I should construct my .mtx file to be used in mri_glmfit. The following variables are what I have used in my fsgd file: GroupDescriptorFile 1,,,, Title Study,,,, Class B,,,, Class NB,,,, Variables ,,,Gender,Age Input, Sub_ID,NB,F,71 Input, Sub_ID, B, F, 80 Please let me know if you need more?information on my work. Thank you! All?the best, Alex Job _______________________________________________ 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/20200427/b… ------------------------------ Message: 13 Date: Mon, 27 Apr 2020 11:10:00 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Mri_segstats for PET data: Reviewer question To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <031794e9-7500-3a7a-975f-0976861333fa(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" An ROI does not have a GM probabability, so I'm not sure what to say. Perhaps he/she wants the average amount of GM in the ROI relative to the size of the ROI? You can get this with mri_compute_volume_fractions. This will produce maps of the GM fraction in each voxel (separating cortical and subcortical). Just use mri_segstats in the same way you used it for the PET. The output will be the fraction of the ROI that is GM. On 4/24/2020 8:41 AM, Shane Schofield wrote: ????????External Email - Use Caution Hi Freesurfer Team, I have used mri_segstats to get ythe?mean PET uptake across all the parcellations in the WMPARC space. These values were calculated in the native PET space (following the DTI tutorial).?A reviewer asked what is the grey matter probability of the ROI and I am not sure how to address this. Any help is kindly appreciated. Thanks. _______________________________________________ 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/20200427/4… ------------------------------ Message: 14 Date: Mon, 27 Apr 2020 11:11:34 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Freeview surface loading error : MRISread failed To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <ab1b5687-7399-f537-53ac-9cbe7d4a5b55(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" What do you see when you run ls -l $SUBJECTS_DIR/fsaverage/surf/lh.inflated On 4/24/2020 11:55 AM, Sezer, Idil wrote: Hello FreeSurfer developers, I am having an issue viewing a .mgh file I created. Using an output from the fmriprep pipeline, I converted an nii.gz to a .mgh surface : mri_vol2surf --src <participant_ID>_desc-preproc_T1w.nii.gz --<participant_ID> --regheader <participant_ID> --hemi lh I am trying to visualize this surface on an inflated brain using: freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=/Users/idilsezer/Desktop/fmriprep_outputs/test/lh.<participant_ID>.mgh I get an error message saying : MRISread(/Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated): could not open file No such file or directory MRISread failed MRISread(/Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated): could not open file And Freeview?s GUI says : Failed to load Surface /Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated I also tried loading it directly from the GUI instead of the command line, it also doesn?t seem to work unfortunately. FreeSurfer version : freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Platform : mac OS Catalina version 10.15.4 (19E287) Thanks in advance for your help, Best regards, Idil _______________________________________________ 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/20200427/d… ------------------------------ Message: 15 Date: Mon, 27 Apr 2020 11:12:28 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] How is Total cortical gray matter volume calculated To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <1961eba0-dfe0-0e92-31b7-394cb425132f(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"; format=flowed The volume between the surfaces is calculated On 4/25/2020 2:56 AM, Ian Hardingham wrote: External Email - Use Caution Morning Freesurfers. Can you describe how the FS stat Total cortical gray matter volume is calculated from the files in the freesurfer subject directory?? Is there an mgz file where each voxel has an estimated percentage grey matter here as the value... or is the volume between the surfaces calculated somehow? Thanks, Ian _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ------------------------------ Message: 16 Date: Mon, 27 Apr 2020 11:15:20 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] correcting fsaverage surface area by eICV To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <712a9f0a-1adc-5a41-afca-3d0403c73662(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Yes, you can do it that way. I'm not sure Ive seen a paper that does it. On 4/27/2020 2:15 AM, Paul wrote: ????????External Email - Use Caution Dear FreeSurfer Developers, To apply the proportion method to correct for head size for subcortical volumes the volume is divided by the eICV. To correct for eICV for surface area using the proportion method, is there any problem using mri_concat to multiple lh.area.10.fsaverage.mgh by 1/eICV and then use the output in qdec/mri_glm_fit? If this is ok, could you please let me know if there are any references where someone has done this? Thanks, Paul _______________________________________________ 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/20200427/e… ------------------------------ Message: 17 Date: Mon, 27 Apr 2020 11:16:17 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Dear professor To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9f146727-530a-d03c-af92-fecb81825469(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" You should use mris_convert. What is your command line and terminal output? On 4/27/2020 11:05 AM, ??? wrote: ????????External Email - Use Caution Dear professor: ? ? I have a question to consult you. I have used the software CAT loaded in matlab to calculate the local gyrification index (LGI) and obtain a .gii file. But I want to use DODS model in freesurfer to statistics the LGI, so now I have to convert the .gii file into .mgh file. I have tried the mris_convert in freesurfer to carry out this but it seemed failed, so would you kind to show or tell me how to convert the .gii file to .mgh file? Thank you very much!? I am looking forwards to hear from you. Sincerely, Fulong Xiao _______________________________________________ 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/20200427/3… ------------------------------ Message: 18 Date: Mon, 27 Apr 2020 23:25:48 +0800 (CST) From: ??? <xiaofulong1681(a)163.com> Subject: [Freesurfer] ???????? To: dgreve(a)mgh.harvard.edu Cc: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <4ed0d638.787e.171bc3e8d14.Coremail.xiaofulong1681(a)163.com> Content-Type: text/plain; charset="gbk" External Email - Use Caution for example, here is the lh.gyrification.gii file from CAT calculation. I want a mgh file called lh.gyrification.mgh. My mris_convert command line is as followings: mris_convert lh.gyrification.gii lh.gyrification.mgh But this mgh file seemed failed. I do not know whether my command line is right or not. You should use mris_convert. What is your command line and terminal output? On 4/27/2020 11:05 AM, ??? wrote: External Email - Use Caution Dear professor: I have a question to consult you. I have used the software CAT loaded in matlab to calculate the local gyrification index (LGI) and obtain a .gii file. But I want to use DODS model in freesurfer to statistics the LGI, so now I have to convert the .gii file into .mgh file. I have tried the mris_convert in freesurfer to carry out this but it seemed failed, so would you kind to show or tell me how to convert the .gii file to .mgh file? Thank you very much! I am looking forwards to hear from you. Sincerely, Fulong Xiao -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200427/4… ------------------------------ Message: 19 Date: Mon, 27 Apr 2020 15:50:18 +0000 From: "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <MN2PR04MB5757E9CFAD27E63C7CC732458AAF0(a)MN2PR04MB5757.namprd04.prod.outlook.com> Content-Type: text/plain; charset="us-ascii" Hi Maria Gabriela - This does not look like a diffusion dicom: PulseSeq tfl_me3d4_16ns Protocol T1 a.y ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Figueiro Longo, Maria Gabriela <MFIGUEIROLONGO(a)mgh.harvard.edu> Sent: Monday, April 27, 2020 9:49 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors Hi, I have been trying different ways to troubleshooting this error without success. I am pasting here the whole error when I try to run "trac-all -prep -c" in the Dev version: INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon INFO: Diffusion root is /autofs/cluster/guptagp/gabi/tracula/Output Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/dev INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864 trac-preproc -c /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/dmrirc.local -log /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.log -cmd /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.cmd ; trac-preproc -c /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/dmrirc.local -log /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.log -cmd /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.cmd ; #------------------------------------- /usr/local/freesurfer/dev/bin/trac-preproc #------------------------------------- #@# Image corrections Mon Apr 27 09:37:59 EDT 2020 mri_convert --bvec-voxel /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz mri_convert --bvec-voxel /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz reading from /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010... Getting Series No INFO: Found 5211 files in /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715 INFO: Scanning for Series Number 102 Scanning Directory INFO: found 140 files in series INFO: loading series header info. RunNo = 101 INFO: sorting. sdfiSameSlicePos() eps = 0.000001 WARNING: file /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ... INFO: (256 256 140), nframes = 1, ismosaic=0 sdfi->UseSliceScaleFactor 0 INFO: rescale not needed datatype = 4, short=4, float=3 PE Dir ROW ROW FileName /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName 3LT050_s1_170715 Date and time StudyDate 20170715 StudyTime 092536.870000 SeriesTime 100956.320000 AcqTime 093429.902500 Acquisition parameters PulseSeq tfl_me3d4_16ns Protocol T1 PhEncDir ROW EchoNo 1 FlipAngle 7 EchoTime 1.69 InversionTime 1100 RepetitionTime 2530 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 101 SeriesNo 102 ImageNo 139 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 54.1349 92.6115 176.0819 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 140 Vc 0.0934 -0.9338 -0.3453 Vr 0.0226 0.3487 -0.9370 Vs 0.4326 0.3520 -0.8301 VolCenter 99.2585 42.3521 -46.1506 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 INFO: no Siemens slice order reversal detected (good!). TR=2530.00, TE=1.69, TI=1100.00, flip angle=7.00 i_ras = (0.0933703, -0.933839, -0.345291) j_ras = (0.0225973, 0.348705, -0.93696) k_ras = (0.432568, 0.35197, -0.830061) writing to /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz... mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat ERROR: Must specify input table of gradient vectors Linux deqi.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Apr 27 09:39:14 EDT 2020 #------------------------------------- /usr/local/freesurfer/dev/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Mon Apr 27 09:39:14 EDT 2020 cp /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat\u2019: No such file or directory cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat\u2019: No such file or directory Linux deqi.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Apr 27 09:39:14 EDT 2020 [deqi:Scripts] (nmr-dev-env) mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat [deqi:Scripts] (nmr-dev-env) mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat [deqi:Scripts] (nmr-dev-env) autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat: Command not found. [deqi:Scripts] (nmr-dev-env) cp autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms cp: cannot stat \u2018autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat\u2019: No such file or directory cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat\u2019: No such file or directory Thanks for the help, Gabriela ________________________________ From: Figueiro Longo, Maria Gabriela Sent: Friday, April 24, 2020 10:47 AM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Tracula error: ERROR: Must specify input table of gradient vectors Hello Dear Freesurfer Developers, I am attempting to run Tracula in the last to subject of my study (I had processed all the other subjects using the same script without problems). However, when I try to run the scrip bellow, I am having the error: " ERROR: Must specify input table of gradient vectors " I am reviewed the associated DICOM images and couldn't find any problem with the images. I reviewed a couple emails in the list, but couldn't find a clear reason for keeping having this error. I am using the Freesurfer Dev version. I really appreciate any help. Thank you, Gabriela # FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon # Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output # Subject IDs (one per time point per subject) # set subjlist = ( 3LT050_s1_170715 ) # Longitudinal base template subject IDs (one for each time point above) # set baselist = ( 3LT050 ) # In case you want to analyze only Huey and Louie # Default: Run analysis on all time points and subjects # # set runlist = (1 2 5 6) # Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data set dcmlist = ( 3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.20170715092715598296003 ) Gabriela Longo, MD, MSc. Emergency Radiology Clinical Fellow, Emergency Radiology Division Massachusetts General Hospital (MGH) mfigueirolongo(a)mgh.harvard.edu Phone: +1 857 214 0568 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200427/5… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 194, Issue 45 *******************************************

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Freesurfer April 2020