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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@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
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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)
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Message: 1 Date: Sun, 26 Apr 2020 12:03:06 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261157500.6647@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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exporting segmented mgz file To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261203210.6647@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
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Message: 3 Date: Sun, 26 Apr 2020 15:57:57 +0000 From: COLLEEN PLETCHER ccpletcher@medicine.wisc.edu Subject: Re: [Freesurfer] Infant freesurfer To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 6E02A4C7-7B9E-4929-9CD4-DEDB93A40E64@medicine.wisc.edu Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
That would be great, thank you!
Colleen Pletcher colleen@tpck.net
On Apr 24, 2020, at 3:58 PM, Lilla Zollei lzollei@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 3:02 PM To: Freesurfer support list freesurfer@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 2:26 PM To: Freesurfer support list freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 4 Date: Sun, 26 Apr 2020 15:32:25 -0700 From: Devavrat Vartak PhD dvartak@berkeley.edu Subject: [Freesurfer] Threshold values changed/modified before display. To: freesurfer@nmr.mgh.harvard.edu Message-ID: CANfw89fO7JtmzL8TJ4cT1UW6seh3OPKBqJasNq0uuBz1sPj3Sg@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/20200426/14...
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Message: 5 Date: Sun, 26 Apr 2020 18:43:29 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Threshold values changed/modified before display. To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261843030.6647@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
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Message: 6 Date: Sun, 26 Apr 2020 23:28:39 +0000 From: "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" vzeng@bidmc.harvard.edu Subject: Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 1587943718956.58079@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261930480.6647@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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@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@gmx.com Subject: [Freesurfer] correcting fsaverage surface area by eICV To: freesurfer@nmr.mgh.harvard.edu Message-ID: trinity-5d777bd5-eae6-4a0b-8e07-75552a04faf6-1587968145560@3c-app-mailcom-bs01
Content-Type: text/plain; charset="us-ascii"
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Message: 9 Date: Mon, 27 Apr 2020 13:49:35 +0000 From: "Figueiro Longo, Maria Gabriela" MFIGUEIROLONGO@mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: MN2PR04MB71356CD2F7B0BEFCF05A34CF92AF0@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@nmr.mgh.harvard.edu freesurfer@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@mgh.harvard.edu
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Message: 10 Date: Mon, 27 Apr 2020 11:00:33 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Overlapping Treatments and fsgd files To: freesurfer@nmr.mgh.harvard.edu Message-ID: be280c60-71d0-f32e-b3d5-69b2f2a8b55d@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:
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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@gmail.com mailto:mrpeverill@gmail.com (preferred) pronouns: he/his
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Message: 11 Date: Mon, 27 Apr 2020 23:05:44 +0800 (CST) From: ??? xiaofulong1681@163.com Subject: [Freesurfer] Dear professor To: freesurfer@nmr.mgh.harvard.edu Message-ID: 323d0afc.a015.171bc2c310d.Coremail.xiaofulong1681@163.com Content-Type: text/plain; charset="gbk"
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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/20200427/8d...
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Message: 12 Date: Mon, 27 Apr 2020 11:06:43 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Contrast file to be used in mri_glimfit To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5d1343c3-f806-5214-55a0-4055719148d0@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:
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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@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
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Message: 13 Date: Mon, 27 Apr 2020 11:10:00 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Mri_segstats for PET data: Reviewer question To: freesurfer@nmr.mgh.harvard.edu Message-ID: 031794e9-7500-3a7a-975f-0976861333fa@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:
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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.
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Message: 14 Date: Mon, 27 Apr 2020 11:11:34 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Freeview surface loading error : MRISread failed To: freesurfer@nmr.mgh.harvard.edu Message-ID: ab1b5687-7399-f537-53ac-9cbe7d4a5b55@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
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Message: 15 Date: Mon, 27 Apr 2020 11:12:28 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] How is Total cortical gray matter volume calculated To: freesurfer@nmr.mgh.harvard.edu Message-ID: 1961eba0-dfe0-0e92-31b7-394cb425132f@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
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Message: 16 Date: Mon, 27 Apr 2020 11:15:20 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] correcting fsaverage surface area by eICV To: freesurfer@nmr.mgh.harvard.edu Message-ID: 712a9f0a-1adc-5a41-afca-3d0403c73662@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:
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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
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Message: 17 Date: Mon, 27 Apr 2020 11:16:17 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Dear professor To: freesurfer@nmr.mgh.harvard.edu Message-ID: 9f146727-530a-d03c-af92-fecb81825469@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:
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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
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Message: 18 Date: Mon, 27 Apr 2020 23:25:48 +0800 (CST) From: ??? xiaofulong1681@163.com Subject: [Freesurfer] ???????? To: dgreve@mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: 4ed0d638.787e.171bc3e8d14.Coremail.xiaofulong1681@163.com Content-Type: text/plain; charset="gbk"
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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/20200427/49...
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Message: 19 Date: Mon, 27 Apr 2020 15:50:18 +0000 From: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: MN2PR04MB5757E9CFAD27E63C7CC732458AAF0@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Figueiro Longo, Maria Gabriela MFIGUEIROLONGO@mgh.harvard.edu Sent: Monday, April 27, 2020 9:49 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@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@nmr.mgh.harvard.edu freesurfer@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@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/20200427/5f...
------------------------------
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 194, Issue 45 *******************************************
You can use --meltzer BinThresh MaskThresh NDil BinThresh is the threshold used to binarize the GM+WM PVF image before any smoothing NDil is the number of times this mask is dialted MaskThresh excludes voxels based on GM+WM PVF after smoothing
There is also --rbv (region-based voxel-wise). There is a hidden option called --lgtm which does a "local" GTM by just doing a correction at a voxel based on the surrounding voxels.
On 4/27/2020 12:36 PM, Ferraro, Pilar wrote:
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@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
Send Freesurfer mailing list submissions to freesurfer@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@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261157500.6647@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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exporting segmented mgz file To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261203210.6647@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@medicine.wisc.edu Subject: Re: [Freesurfer] Infant freesurfer To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 6E02A4C7-7B9E-4929-9CD4-DEDB93A40E64@medicine.wisc.edu Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
That would be great, thank you!
Colleen Pletcher colleen@tpck.net
On Apr 24, 2020, at 3:58 PM, Lilla Zollei lzollei@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 3:02 PM To: Freesurfer support list freesurfer@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 2:26 PM To: Freesurfer support list freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Message: 4 Date: Sun, 26 Apr 2020 15:32:25 -0700 From: Devavrat Vartak PhD dvartak@berkeley.edu Subject: [Freesurfer] Threshold values changed/modified before display. To: freesurfer@nmr.mgh.harvard.edu Message-ID: CANfw89fO7JtmzL8TJ4cT1UW6seh3OPKBqJasNq0uuBz1sPj3Sg@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).
- Does freeview recaluate/modify the values before they are displayed?
- Is it possible to display the values of the overlay as they are?
Thank you. Stay healthy and safe!
Best, Devavrat
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@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edumailto: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@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261157500.6647@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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exporting segmented mgz file To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261203210.6647@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@medicine.wisc.edu Subject: Re: [Freesurfer] Infant freesurfer To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 6E02A4C7-7B9E-4929-9CD4-DEDB93A40E64@medicine.wisc.edu Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
That would be great, thank you!
Colleen Pletcher colleen@tpck.net
On Apr 24, 2020, at 3:58 PM, Lilla Zollei lzollei@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 3:02 PM To: Freesurfer support list freesurfer@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 2:26 PM To: Freesurfer support list freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 4 Date: Sun, 26 Apr 2020 15:32:25 -0700 From: Devavrat Vartak PhD dvartak@berkeley.edu Subject: [Freesurfer] Threshold values changed/modified before display. To: freesurfer@nmr.mgh.harvard.edu Message-ID: CANfw89fO7JtmzL8TJ4cT1UW6seh3OPKBqJasNq0uuBz1sPj3Sg@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!
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Message: 5 Date: Sun, 26 Apr 2020 18:43:29 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Threshold values changed/modified before display. To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261843030.6647@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
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Message: 6 Date: Sun, 26 Apr 2020 23:28:39 +0000 From: "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" vzeng@bidmc.harvard.edu Subject: Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 1587943718956.58079@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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.
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Message: 7 Date: Sun, 26 Apr 2020 19:31:53 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261930480.6647@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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@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@gmx.com Subject: [Freesurfer] correcting fsaverage surface area by eICV To: freesurfer@nmr.mgh.harvard.edu Message-ID: trinity-5d777bd5-eae6-4a0b-8e07-75552a04faf6-1587968145560@3c-app-mailcom-bs01
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Message: 9 Date: Mon, 27 Apr 2020 13:49:35 +0000 From: "Figueiro Longo, Maria Gabriela" MFIGUEIROLONGO@mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: MN2PR04MB71356CD2F7B0BEFCF05A34CF92AF0@MN2PR04MB7135.namprd04.prod.outlook.com
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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@nmr.mgh.harvard.edu freesurfer@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@mgh.harvard.edu
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Message: 10 Date: Mon, 27 Apr 2020 11:00:33 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Overlapping Treatments and fsgd files To: freesurfer@nmr.mgh.harvard.edu Message-ID: be280c60-71d0-f32e-b3d5-69b2f2a8b55d@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@gmail.com mailto:mrpeverill@gmail.com (preferred) pronouns: he/his
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Message: 11 Date: Mon, 27 Apr 2020 23:05:44 +0800 (CST) From: ??? xiaofulong1681@163.com Subject: [Freesurfer] Dear professor To: freesurfer@nmr.mgh.harvard.edu Message-ID: 323d0afc.a015.171bc2c310d.Coremail.xiaofulong1681@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/20200427/8d...
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Message: 12 Date: Mon, 27 Apr 2020 11:06:43 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Contrast file to be used in mri_glimfit To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5d1343c3-f806-5214-55a0-4055719148d0@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@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
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Message: 13 Date: Mon, 27 Apr 2020 11:10:00 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Mri_segstats for PET data: Reviewer question To: freesurfer@nmr.mgh.harvard.edu Message-ID: 031794e9-7500-3a7a-975f-0976861333fa@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.
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Message: 14 Date: Mon, 27 Apr 2020 11:11:34 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Freeview surface loading error : MRISread failed To: freesurfer@nmr.mgh.harvard.edu Message-ID: ab1b5687-7399-f537-53ac-9cbe7d4a5b55@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
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Message: 15 Date: Mon, 27 Apr 2020 11:12:28 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] How is Total cortical gray matter volume calculated To: freesurfer@nmr.mgh.harvard.edu Message-ID: 1961eba0-dfe0-0e92-31b7-394cb425132f@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
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Message: 16 Date: Mon, 27 Apr 2020 11:15:20 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] correcting fsaverage surface area by eICV To: freesurfer@nmr.mgh.harvard.edu Message-ID: 712a9f0a-1adc-5a41-afca-3d0403c73662@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
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Message: 17 Date: Mon, 27 Apr 2020 11:16:17 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Dear professor To: freesurfer@nmr.mgh.harvard.edu Message-ID: 9f146727-530a-d03c-af92-fecb81825469@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
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Message: 18 Date: Mon, 27 Apr 2020 23:25:48 +0800 (CST) From: ??? xiaofulong1681@163.com Subject: [Freesurfer] ???????? To: dgreve@mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: 4ed0d638.787e.171bc3e8d14.Coremail.xiaofulong1681@163.com Content-Type: text/plain; charset="gbk"
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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/20200427/49...
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Message: 19 Date: Mon, 27 Apr 2020 15:50:18 +0000 From: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: MN2PR04MB5757E9CFAD27E63C7CC732458AAF0@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Figueiro Longo, Maria Gabriela MFIGUEIROLONGO@mgh.harvard.edu Sent: Monday, April 27, 2020 9:49 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@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@nmr.mgh.harvard.edu freesurfer@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@mgh.harvard.edu
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End of Freesurfer Digest, Vol 194, Issue 45 *******************************************
Did you get this answer yesterday?
On 4/27/2020 12:48 PM, Douglas N. Greve wrote:
You can use --meltzer BinThresh MaskThresh NDil BinThresh is the threshold used to binarize the GM+WM PVF image before any smoothing NDil is the number of times this mask is dialted MaskThresh excludes voxels based on GM+WM PVF after smoothing
There is also --rbv (region-based voxel-wise). There is a hidden option called --lgtm which does a "local" GTM by just doing a correction at a voxel based on the surrounding voxels.
On 4/28/2020 1:58 PM, Ferraro, Pilar wrote:
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@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
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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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261157500.6647@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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exporting segmented mgz file To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261203210.6647@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@medicine.wisc.edu Subject: Re: [Freesurfer] Infant freesurfer To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 6E02A4C7-7B9E-4929-9CD4-DEDB93A40E64@medicine.wisc.edu Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
That would be great, thank you!
Colleen Pletcher colleen@tpck.net
On Apr 24, 2020, at 3:58 PM, Lilla Zollei lzollei@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 3:02 PM To: Freesurfer support list freesurfer@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 2:26 PM To: Freesurfer support list freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Message: 4 Date: Sun, 26 Apr 2020 15:32:25 -0700 From: Devavrat Vartak PhD dvartak@berkeley.edu Subject: [Freesurfer] Threshold values changed/modified before display. To: freesurfer@nmr.mgh.harvard.edu Message-ID: CANfw89fO7JtmzL8TJ4cT1UW6seh3OPKBqJasNq0uuBz1sPj3Sg@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).
- Does freeview recaluate/modify the values before they are displayed?
- Is it possible to display the values of the overlay as they are?
Thank you. Stay healthy and safe!
Best, Devavrat
External Email - Use Caution
Hi Freesurfer experts,
Unfortunately I was unable to see the answer to my message. Would you be able to forward it to me again?
Many thanks,
Pilar
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@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu ha scritto:
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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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261157500.6647@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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] exporting segmented mgz file To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261203210.6647@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@medicine.wisc.edu Subject: Re: [Freesurfer] Infant freesurfer To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 6E02A4C7-7B9E-4929-9CD4-DEDB93A40E64@medicine.wisc.edu Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
That would be great, thank you!
Colleen Pletcher colleen@tpck.net
On Apr 24, 2020, at 3:58 PM, Lilla Zollei lzollei@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 3:02 PM To: Freesurfer support list freesurfer@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lilla Zollei lzollei@nmr.mgh.harvard.edu Sent: Wednesday, April 22, 2020 2:26 PM To: Freesurfer support list freesurfer@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@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
Message: 4 Date: Sun, 26 Apr 2020 15:32:25 -0700 From: Devavrat Vartak PhD dvartak@berkeley.edu Subject: [Freesurfer] Threshold values changed/modified before display. To: freesurfer@nmr.mgh.harvard.edu Message-ID: CANfw89fO7JtmzL8TJ4cT1UW6seh3OPKBqJasNq0uuBz1sPj3Sg@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/20200426/14...
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Message: 5 Date: Sun, 26 Apr 2020 18:43:29 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Threshold values changed/modified before display. To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261843030.6647@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@bidmc.harvard.edu Subject: Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 1587943718956.58079@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] Re: Intensity inhomogeneity messing with the wm.mgz To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.2004261930480.6647@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@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@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@gmx.com Subject: [Freesurfer] correcting fsaverage surface area by eICV To: freesurfer@nmr.mgh.harvard.edu Message-ID: trinity-5d777bd5-eae6-4a0b-8e07-75552a04faf6-1587968145560@3c-app-mailcom-bs01
Content-Type: text/plain; charset="us-ascii"
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Message: 9 Date: Mon, 27 Apr 2020 13:49:35 +0000 From: "Figueiro Longo, Maria Gabriela" MFIGUEIROLONGO@mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: MN2PR04MB71356CD2F7B0BEFCF05A34CF92AF0@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@nmr.mgh.harvard.edu freesurfer@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@mgh.harvard.edu
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Message: 10 Date: Mon, 27 Apr 2020 11:00:33 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Overlapping Treatments and fsgd files To: freesurfer@nmr.mgh.harvard.edu Message-ID: be280c60-71d0-f32e-b3d5-69b2f2a8b55d@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:
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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@gmail.com mailto:mrpeverill@gmail.com (preferred) pronouns: he/his
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Message: 11 Date: Mon, 27 Apr 2020 23:05:44 +0800 (CST) From: ??? xiaofulong1681@163.com Subject: [Freesurfer] Dear professor To: freesurfer@nmr.mgh.harvard.edu Message-ID: 323d0afc.a015.171bc2c310d.Coremail.xiaofulong1681@163.com Content-Type: text/plain; charset="gbk"
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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/20200427/8d...
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Message: 12 Date: Mon, 27 Apr 2020 11:06:43 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Contrast file to be used in mri_glimfit To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5d1343c3-f806-5214-55a0-4055719148d0@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:
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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@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
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Message: 13 Date: Mon, 27 Apr 2020 11:10:00 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Mri_segstats for PET data: Reviewer question To: freesurfer@nmr.mgh.harvard.edu Message-ID: 031794e9-7500-3a7a-975f-0976861333fa@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:
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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.
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Message: 14 Date: Mon, 27 Apr 2020 11:11:34 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Freeview surface loading error : MRISread failed To: freesurfer@nmr.mgh.harvard.edu Message-ID: ab1b5687-7399-f537-53ac-9cbe7d4a5b55@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
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Message: 15 Date: Mon, 27 Apr 2020 11:12:28 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] How is Total cortical gray matter volume calculated To: freesurfer@nmr.mgh.harvard.edu Message-ID: 1961eba0-dfe0-0e92-31b7-394cb425132f@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
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Message: 16 Date: Mon, 27 Apr 2020 11:15:20 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] correcting fsaverage surface area by eICV To: freesurfer@nmr.mgh.harvard.edu Message-ID: 712a9f0a-1adc-5a41-afca-3d0403c73662@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:
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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
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Message: 17 Date: Mon, 27 Apr 2020 11:16:17 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Dear professor To: freesurfer@nmr.mgh.harvard.edu Message-ID: 9f146727-530a-d03c-af92-fecb81825469@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:
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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
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Message: 18 Date: Mon, 27 Apr 2020 23:25:48 +0800 (CST) From: ??? xiaofulong1681@163.com Subject: [Freesurfer] ???????? To: dgreve@mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: 4ed0d638.787e.171bc3e8d14.Coremail.xiaofulong1681@163.com Content-Type: text/plain; charset="gbk"
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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:
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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/20200427/49...
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Message: 19 Date: Mon, 27 Apr 2020 15:50:18 +0000 From: "Yendiki, Anastasia" AYENDIKI@mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Message-ID: MN2PR04MB5757E9CFAD27E63C7CC732458AAF0@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@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Figueiro Longo, Maria Gabriela MFIGUEIROLONGO@mgh.harvard.edu Sent: Monday, April 27, 2020 9:49 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@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@nmr.mgh.harvard.edu freesurfer@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@mgh.harvard.edu
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