External Email - Use Caution
Hi Freesurfer experts,
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 ha scritto:
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When replying, please edit your Subject line so it is more specific
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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>try
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
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 Freesurferthat
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
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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>
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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
Phone: +1 857 214 0568
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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
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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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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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"
External Email - Use Caution
for example, here is the lh.gyrification.gii file from CAT calculation. I want a mgh file called lh.gyrification.mgh. My mris_convert command line is as followings:
mris_convert lh.gyrification.gii lh.gyrification.mgh
But this mgh file seemed failed. I do not know whether my command line is right or not.
You should use mris_convert. What is your command line and terminal output?
On 4/27/2020 11:05 AM, ??? wrote:
External Email - Use Caution
Dear professor:
I have a question to consult you. I have used the software CAT loaded in matlab to calculate the local gyrification index (LGI) and obtain a .gii file. But I want to use DODS model in freesurfer to statistics the LGI, so now I have to convert the .gii file into .mgh file. I have tried the mris_convert in freesurfer to carry out this but it seemed failed, so would you kind to show or tell me how to convert the .gii file to .mgh file? Thank you very much! I am looking forwards to hear from you.
Sincerely, Fulong Xiao
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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
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