[Freesurfer] Longitudinal TRACULA Thalamic segmentation failure

[Brendan Angelo]

External Email - Use Caution

Hi experts,

I have been attempting to analyze a group of subjects through the longitudinal 
TRACULA pipeline and have run into many issues regarding the preprocessing step 
making use of the thalamic segmentation. I've combed through the archives on 
this topic and have found many different threads relating to issues with the 
necessary files for the thalamic segmentation not being created, particularly 
the aparc+aseg+thalnuc.nii.gz file during the trac-all -prep step.

I am attempting these analyses on a newer Mac Studio computer and cannot make 
use of the MATLAB 2014b runtime to segment the thalamus with the old script. 
Using the suggestions from 
this
 previous question, I ran the segment_subregions thalamus python script and 
renamed all the outputs to match the MATLAB outputs 
(ThalamicNuclei.v12.T1.FSvoxelSpace.mgz, ThalamicNuclei.v12.T1.mgz, 
ThalamicNuclei.v12.T1.volumes.txt), but still ran into errors with the prep 
script and creation of the aparc+aseg+thalnuc.nii.gz file mentioned above.

It seems like all the previous threads on this issue result in no permanent 
solution, are there any suggestions on ways to fix this, at least temporarily? 
Any discussion on this topic would be appreciated. I've also attached the log 
files from one of my failed runs, as well as the TRACULA configuration file. 
This was all done on Freesurfer 7.4.1.

Thanks,
Brendan

Brendan Angelo, MS
BRANCH Lab
USC


tracula.long.config
Description: tracula.long.config


trac-all.log
Description: trac-all.log


trac-all.error
Description: trac-all.error
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[Freesurfer] Longitudinal TRACULA subject folder confusion

[Brendan Angelo]

External Email - Use Caution

Hello FreeSurfer devs,

I am attempting to run a Longitudinal TRACULA analysis on 3 timepoints per 
subject using an HCP server. I have used the example dmrirc page 
(https://secure-web.cisco.com/1JykEBcpM6vAD_4qy69NGW33wNc83B-TuXM37yVrgXaTHoNwBQkiBWLQw7KKEy6uEbNEAK9R1mVoohAnT91b81Y95fEpezV5Esc-exSdzLMxJ725HRD8_ZRJzk7ELJgS-K3TxVCpCzoboUfe-9K8gAOHgiGXZ_OoJwul4ci0lr2_F6U0uDGjgXK8_3G-oK4NzwUA-zeJnQkvD1AFkCq7h92Rt1KR2DTJdIF0NcpetKomJ8_3Pfalai9v4py_wVjEB73Xfb9dCDS8mdP82g6izgsjg3uRWCO61wh72zYwTB02alYFtGZfZB92Sed6faiO4HW53u19StCczTQslWduBfw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fdmrirc%23Example2.3ALongitudinalstudy.2Conediffusionscanpersession)
 to create a configuration file to be fed into the trac-all command, but I am 
running into issues with the naming of folders containing each subject and 
their respective FS timepoints.

I have attached my configuration file, as well as a log output from one subject 
run for reference, but the issues I am running into pertain to the directory 
names of each subject and the FS timepoint needed for the longitudinal 
analysis. When I follow the example configuration file, it notes that each 
subject should be listed for each number of timepoints that are being included 
(in this case, we have 3 timepoints for each subject, and they are stored as 
{subjID}_Y{0,2,4}). When running trac-all -prep while the FS directory is 
called 100_Y0, for example, this error appears: ERROR: cannot find 
/ifs/loni/faculty/thompson/four_d/bangelo/FS_DTI_longitudinal/100_Y0.long.100_Y0,
 where the FS_DTI_longitudinal directory contains all the completed FS 
recon-all runs for each subject and timepoint.

However, after changing the FS directory name to match the name it is searching 
for, I am met with an additional error after mri_convert is called: ERROR: 
cannot find /ifs/loni/faculty/thompson/four_d/bangelo/FS_DTI_longitudinal/100_Y0

I am extremely confused by this, as the configuration file example does not 
reference having an additional directory for each time point, that isn’t the 
directory that contains the FS output from that timepoint.

Is there a way to force the scripting to only look for 100_Y0, instead of 
100_Y0.long.100_Y0? And what is this additional directory it is looking for? I 
know it is trying to find a folder of the same name that I have set in the 
baselist, but I am still confused why the baselist folder and the subject 
folder are different to the script. Any help with sorting this out and any 
additional information that can be provided about what directories the script 
is looking for and what they should contain would be extremely helpful.

1. FreeSurfer Version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
2. Platform: CentOS version 6 or 7 (I’ve been told both versions when I asked)
3. uname -a: Linux c2002 2.6.32-696.23.1.el6.x86_64 #1 SMP Tue Mar 13 22:44:18 
UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
4. Tracula log file is attached

Thank you!

Sincerely,
Brendan Angelo

Brendan Angelo, MS
BRANCH Lab
USC



dmricr_long_TRACULA
Description: dmricr_long_TRACULA


trac-all.local-copy
Description: trac-all.local-copy


trac-all.log
Description: trac-all.log
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Re: [Freesurfer] longitudinal TRACULA -prep error

[Yendiki, Anastasia]

Hi Carissa – Don’t set variables to “None” in the config file. Just remove 
those lines from the config file altogether – that’s the same as not having any 
inputs for them.

Hope this helps,
a.y

From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Carissa Nicole Weis mailto:cnw...@uwm.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Thursday, September 27, 2018 at 4:28 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] longitudinal TRACULA -prep error


External Email - Use Caution
Hello,

I’m running into an error in the longitudinal TRACULA pipeline that I’m not 
sure how to resolve. I saw this error in the message board but there was no 
resolution to the problem so I thought I’d ask again. I’ve successfully run the 
recon-all longitudinal pipeline and am trying to run the trac-all –prep step 
with a longitudinal configuration file.

Here’s the error, it happens for both time points listed in my configuration 
file:

#@# Image corrections Thu Sep 27 12:59:31 CDT 2018
mri_convert 
/bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1
 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz
mri_convert 
/bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1
 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1...
crypt_gkey = *CyXds2s6sOqQ
Starting DICOMRead2()
dcmfile = 
/bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1
dcmdir = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI
Ref Series No = 6
Found 2666 files, checking for dicoms
Found 2660 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 2
Vs: 0 0 1
Second Sorting
Counting frames
nframes = 38
nslices = 70
ndcmfiles = 2660
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=1.00, TE=57.70, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
writing to 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz...
crypt_gkey = *CyXds2s6sOqQ
mri_probedicom --i 
/bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1
 > /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dcminfo.dat
cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs
cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals
mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.tmp 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs
mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals.tmp 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals
flip4fsl 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 2
fslswapdim 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz x 
-y z 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz
INFO: found 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals,
 converting to FSL format
INFO: found 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs,
 converting to FSL format
mv -f 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvecs
 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs
mv -f 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvals
 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals
eddy_correct 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz
 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz 0
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0001
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0002
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0003
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0004
processing 
/bigraid-

[Freesurfer] longitudinal TRACULA -prep error

[Carissa Nicole Weis]

External Email - Use Caution

Hello,

I'm running into an error in the longitudinal TRACULA pipeline that I'm not 
sure how to resolve. I saw this error in the message board but there was no 
resolution to the problem so I thought I'd ask again. I've successfully run the 
recon-all longitudinal pipeline and am trying to run the trac-all -prep step 
with a longitudinal configuration file.

Here's the error, it happens for both time points listed in my configuration 
file:

#@# Image corrections Thu Sep 27 12:59:31 CDT 2018
mri_convert 
/bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1
 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz
mri_convert 
/bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1
 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1...
crypt_gkey = *CyXds2s6sOqQ
Starting DICOMRead2()
dcmfile = 
/bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1
dcmdir = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI
Ref Series No = 6
Found 2666 files, checking for dicoms
Found 2660 dicom files in series.
First Sorting
Computing Slice Direction
Vs: 0 0 2
Vs: 0 0 1
Second Sorting
Counting frames
nframes = 38
nslices = 70
ndcmfiles = 2660
PE Dir = COL (dicom read)
TransferSyntaxUID: --1.2.840.10008.1.2.1--
Loading pixel data
TR=1.00, TE=57.70, TI=0.00, flip angle=90.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, 1)
writing to 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz...
crypt_gkey = *CyXds2s6sOqQ
mri_probedicom --i 
/bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1
 > /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dcminfo.dat
cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs
cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals
mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.tmp 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs
mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals.tmp 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals
flip4fsl 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz
INFO: input image orientation is LPS
INFO: input image determinant is 2
fslswapdim 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz x 
-y z 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz
INFO: left-right orientation was flipped by fslswapdim
fslorient -forceradiological 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz
INFO: found 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals,
 converting to FSL format
INFO: found 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs,
 converting to FSL format
mv -f 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvecs
 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs
mv -f 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvals
 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals
eddy_correct 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz
 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz 0
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0001
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0002
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0003
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0004
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0005
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0006
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0007
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0008
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0009
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0010
processing 
/bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0011

Re: [Freesurfer] Longitudinal TRACULA study

[Yendiki, Anastasia]

Hi Donatas – All sounds fine. You can process single time points, and you can 
process subsets of time points if the DWI data from one of them is unusable. 
The T1 base template is only used as a reference space for longitudinal 
TRACULA, so it shouldn’t make a huge difference if one additional time point 
was used to generate that T1 base template (assuming of course that there 
wasn’t a huge morphological difference in that specific time point that would 
make the base template much different if it had been generated without that 
time point).

Best,
a.y

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Donatas Sederevicius 
<donatas.sederevic...@psykologi.uio.no<mailto:donatas.sederevic...@psykologi.uio.no>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Wednesday, January 31, 2018 at 4:51 AM
To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Longitudinal TRACULA study

Hi,

I want to clarify some aspects longitudinal TRACULA processing before 
processing my data.

For example, I have 3 timepoints of data of the same participant:

sub101_01
sub101_02
sub101_03

All of these have structural and diffusion data (same scanner, same acquisition 
parameters). I processed structural data using FS longitudinal pipeline and got 
the following:

base_101
sub101_01.long.base_101
sub101_02.long.base_101
sub101_03.long.base_101

Now I want to run longitudinal TRACULA processing. If all data is OK after 
quality checking (struct and DWI) I could set the configuration file as follows:

set subjlist = ( sub101_01 \
 sub101_02 \
 sub101_03 )

set baselist = ( base_101 \
 base_101 \
 base_101 )

It turns out that DWI data of sub101_01 is extremely distorted and cannot be 
used for processing. Should I re-process struct data based on the last two 
timepoints or is it perfectly fine to use the base and long derived from all 
timepoints although I’m running tracula for the last two timepoints of DWI?

In addition to that, is it fine to run longitudinal TRACULA on a list of 
subjects where some of them have only one timepoint of data and structural 
processing underwent longitudinal pipeline for that one timepoint?

Thank you for your answers.

Best,
Donatas
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[Freesurfer] Longitudinal TRACULA study

[Donatas Sederevicius]

Hi,

I want to clarify some aspects longitudinal TRACULA processing before 
processing my data.

For example, I have 3 timepoints of data of the same participant:

sub101_01
sub101_02
sub101_03

All of these have structural and diffusion data (same scanner, same acquisition 
parameters). I processed structural data using FS longitudinal pipeline and got 
the following:

base_101
sub101_01.long.base_101
sub101_02.long.base_101
sub101_03.long.base_101

Now I want to run longitudinal TRACULA processing. If all data is OK after 
quality checking (struct and DWI) I could set the configuration file as follows:

set subjlist = ( sub101_01 \
 sub101_02 \
 sub101_03 )

set baselist = ( base_101 \
 base_101 \
 base_101 )

It turns out that DWI data of sub101_01 is extremely distorted and cannot be 
used for processing. Should I re-process struct data based on the last two 
timepoints or is it perfectly fine to use the base and long derived from all 
timepoints although I’m running tracula for the last two timepoints of DWI?

In addition to that, is it fine to run longitudinal TRACULA on a list of 
subjects where some of them have only one timepoint of data and structural 
processing underwent longitudinal pipeline for that one timepoint?

Thank you for your answers.

Best,
Donatas
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] longitudinal TRACULA

[Yendiki, Anastasia]

Hi Lars – That’s correct, you don’t need to run cross-sectional TRACULA first, 
you just need to run longitudinal recon-all before you run longitudinal 
TRACULA, and it expects that the time points and base template subject IDs are 
the same for recon-all and for TRACULA. It sounds like the time points’ MNI 
registrations were not created, which is something that happens before the 
command that gives you the error. Is there an error in the time points’ 
trac-all.log files?

a.y

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Lars M. Rimol" <lari...@gmail.com<mailto:lari...@gmail.com>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Saturday, July 29, 2017 at 8:31 AM
To: FS maling list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] longitudinal TRACULA

Hi,

I've run cross-sectional TRACULA on one subject, three different timepoints. 
Now I'm trying to run a longitudinal analysis on the same subject's 3 
timepoints. My understanding was that for TRACULA, unlike for morphometry, I 
don't need to first run cross sectional before longitudinal, the only 
requirement is that I have a longitudinal dmrirc file that specifies the 
timepoints with their corresponding files.

It crashed with these error messages:

#@# Inter-subject registration (base template) lø. 29. juli 14:25:45 +0200 2017
cp 
/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat
 
/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat
 /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_base/dmri/xfms
cp: cannot stat 
`/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat':
 No such file or directory
cp: cannot stat 
`/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat':
 No such file or directory
Linux compute-16-32.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux


Any idea what went wrong here?


Thank you!



Sincerely yours,

Lars M. Rimol, PhD
Senior Researcher
Norwegian Advisory Unit for Functional MRI
Department of Radiology
St. Olav's University Hospital
7006 Trondheim
Norway

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] longitudinal TRACULA

[Lars M. Rimol]

Hi,

I've run cross-sectional TRACULA on one subject, three different
timepoints. Now I'm trying to run a longitudinal analysis on the same
subject's 3 timepoints. My understanding was that for TRACULA, unlike for
morphometry, I don't need to first run cross sectional before longitudinal,
the only requirement is that I have a longitudinal dmrirc file that
specifies the timepoints with their corresponding files.

It crashed with these error messages:

#@# Inter-subject registration (base template) lø. 29. juli 14:25:45 +0200
2017
cp
/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat
/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat
/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_base/dmri/xfms
cp: cannot stat
`/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat':
No such file or directory
cp: cannot stat
`/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat':
No such file or directory
Linux compute-16-32.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20
01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux


Any idea what went wrong here?


Thank you!



Sincerely yours,

Lars M. Rimol, PhD
Senior Researcher
Norwegian Advisory Unit for Functional MRI
Department of Radiology
St. Olav's University Hospital
7006 Trondheim
Norway
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] longitudinal tracula error

[Bárbara Avelar Pereira]

Thanks again — it was a huge help!

On 31 Jan 2017, at 18:25, Yendiki, Anastasia 
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Barbara – Thank you for your kind words. As you’ve read, if the output files 
are generated, then you’re good to go. Bedpost does not differentiate between 
longitudinal and cross-sectional data, so it’s run separately on each time 
point’s …/dmri/ folder.

Best,
a.y

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Bárbara Avelar Pereira 
<barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, January 30, 2017 at 10:48 AM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks again for the help! And congrats on tracula — it's a great tool, and the 
online support is really good :)

I do have a follow-up question, if that’s OK. I’m currently running bedpost, 
and it gives the following error:

(…)
53 slices processed
54 slices processed
54 slices processed
55 slices processed
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear to have successfully 
completed. Please examine your results carefully.
/usr/local/freesurfer/bin/bedpostx_mgh: line 345: kill: (21128) - No such 
process

I was not running this on a cluster, but I was running a few subjects at the 
same time so I was wondering if it could be a memory problem? Or a 
compatibility problem between FSL and freesurfer?

It seems strange that it shows the same slice more than once on the monitor. 
But from what I read, the monitor is not entirely reliable and the best way to 
check whether everything ran smoothly is to look at the output. I have all the 
files that should have been created, but I’m still suspicious that something 
might be wrong. For example, my merged_xxx files are 50 volumes (should they 
have the same number of volumes as my original nii file? Because this is not 
the case...).

I’ve also tried running it directly from the command line and the error is the 
same (however, since this is longitudinal, when running bedpost from the 
command line, can I simply run it for each timepoint separately as if it was 
cross-sectional or is there an extra step?)

Many thanks!

On 26 Jan 2017, at 14:51, Yendiki, Anastasia 
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] lon

Re: [Freesurfer] longitudinal tracula error

[Yendiki, Anastasia]

Hi Barbara – Thank you for your kind words. As you’ve read, if the output files 
are generated, then you’re good to go. Bedpost does not differentiate between 
longitudinal and cross-sectional data, so it’s run separately on each time 
point’s …/dmri/ folder.

Best,
a.y

From: 
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Bárbara Avelar Pereira 
<barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>>
Reply-To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Monday, January 30, 2017 at 10:48 AM
To: Freesurfer support list 
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks again for the help! And congrats on tracula — it's a great tool, and the 
online support is really good :)

I do have a follow-up question, if that’s OK. I’m currently running bedpost, 
and it gives the following error:

(…)
53 slices processed
54 slices processed
54 slices processed
55 slices processed
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear to have successfully 
completed. Please examine your results carefully.
/usr/local/freesurfer/bin/bedpostx_mgh: line 345: kill: (21128) - No such 
process

I was not running this on a cluster, but I was running a few subjects at the 
same time so I was wondering if it could be a memory problem? Or a 
compatibility problem between FSL and freesurfer?

It seems strange that it shows the same slice more than once on the monitor. 
But from what I read, the monitor is not entirely reliable and the best way to 
check whether everything ran smoothly is to look at the output. I have all the 
files that should have been created, but I’m still suspicious that something 
might be wrong. For example, my merged_xxx files are 50 volumes (should they 
have the same number of volumes as my original nii file? Because this is not 
the case...).

I’ve also tried running it directly from the command line and the error is the 
same (however, since this is longitudinal, when running bedpost from the 
command line, can I simply run it for each timepoint separately as if it was 
cross-sectional or is there an extra step?)

Many thanks!

On 26 Jan 2017, at 14:51, Yendiki, Anastasia 
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-r

Re: [Freesurfer] longitudinal tracula error

[Bárbara Avelar Pereira]

Hi Anastasia,

Thanks again for the help! And congrats on tracula — it's a great tool, and the 
online support is really good :)

I do have a follow-up question, if that’s OK. I’m currently running bedpost, 
and it gives the following error:

(…)
53 slices processed
54 slices processed
54 slices processed
55 slices processed
Queuing post processing stage
64 slices processed
For some reason the bedpostX process DOES NOT appear to have successfully 
completed. Please examine your results carefully.
/usr/local/freesurfer/bin/bedpostx_mgh: line 345: kill: (21128) - No such 
process

I was not running this on a cluster, but I was running a few subjects at the 
same time so I was wondering if it could be a memory problem? Or a 
compatibility problem between FSL and freesurfer?

It seems strange that it shows the same slice more than once on the monitor. 
But from what I read, the monitor is not entirely reliable and the best way to 
check whether everything ran smoothly is to look at the output. I have all the 
files that should have been created, but I’m still suspicious that something 
might be wrong. For example, my merged_xxx files are 50 volumes (should they 
have the same number of volumes as my original nii file? Because this is not 
the case...).

I’ve also tried running it directly from the command line and the error is the 
same (however, since this is longitudinal, when running bedpost from the 
command line, can I simply run it for each timepoint separately as if it was 
cross-sectional or is there an extra step?)

Many thanks!

On 26 Jan 2017, at 14:51, Yendiki, Anastasia 
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia 
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file s

Re: [Freesurfer] longitudinal tracula error

[Yendiki, Anastasia]

Glad to hear it, thanks for checking! If the final 6.0 works, there's no need 
to dig up the beta.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Thursday, January 26, 2017 3:29 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia 
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.

Re: [Freesurfer] longitudinal tracula error

[Bárbara Avelar Pereira]

Hi Anastasia,

Thanks so much for your help! Sorry for the delay in replying -- just wanted to 
make sure the was problem was indeed solved. Since I'm using a server for which 
I have no administrative rights, I had to wait before the update was installed. 
It seems to run perfectly now.
I can't find the beta version I was using at the time (just deleted it once I 
realised I was having the same problem), but if I manage to trace it back, I'll 
let you know.

Once again, thanks, I'm super grateful!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Yendiki, Anastasia 
[ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>]
Sent: Sunday, January 22, 2017 7:33 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia 
<ayend...@mgh.harvard.edu<mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

From the mailing list, it seems a similar issue has been fixed in previous 
updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, it asks for it: ERROR: 
cannot find /

Re: [Freesurfer] longitudinal tracula error

[Yendiki, Anastasia]

Hi Barbara - If you're using the 5.3 version, then you'll have to download the 
update from 2014:
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

This should fix the problem. But if there's a version of the 6.0 beta that was 
having the same problem, please let me know (by sending the trac-all copy of 
that version) so I can fix that asap.

Thanks!

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 7:00 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] longitudinal tracula error

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia <ayend...@mgh.harvard.edu> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

>From the mailing list, it seems a similar issue has been fixed in previous 
>updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, it asks for it: ERROR: 
cannot find /Documents/TRACULA/TEST/S0001.01

>From what I understand, the base is not necessary to run any analysis, but it 
>has to be there anyhow (?): 
>https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html 
>Maybe I am understanding this incorrectly?

Since the base is used to create the longitudinal output (*long*), including 
the aparc+aseg.mgz file, and those are then used in tracula, I thought I could 
run things without it. I decided to take out the “set baselist” part from the 
configuration file — this way it seems to run fine (so far). But I assume it’s 
there for a reason so I’m not sure this is a solution at all...

Any help would be much appreciated!

Details:
1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) platform: CentOS release 6.8 (Final)
3) Operating system details (kernel name, release, version, etc.): Linux 
2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 
x86_64 GNU/Linux
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.

Re: [Freesurfer] longitudinal tracula error

[Bárbara Avelar Pereira]

Hi Anastasia,

Thanks so much for your quick reply. I've only tried version 6.0 to determine 
whether the error was possibly version-related, but that doesn’t seem to be the 
case… I'm actually working with version 5.3 so I'll send attach the 
trac-all.local-copy for that if that’s OK. Once again, thank you!

On 20 Jan 2017, at 23:52, Yendiki, Anastasia <ayend...@mgh.harvard.edu> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>]
 on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se<mailto:barbara.avelar.pere...@ki.se>]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

>From the mailing list, it seems a similar issue has been fixed in previous 
>updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, it asks for it: ERROR: 
cannot find /Documents/TRACULA/TEST/S0001.01

>From what I understand, the base is not necessary to run any analysis, but it 
>has to be there anyhow (?): 
>https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html 
>Maybe I am understanding this incorrectly?

Since the base is used to create the longitudinal output (*long*), including 
the aparc+aseg.mgz file, and those are then used in tracula, I thought I could 
run things without it. I decided to take out the “set baselist” part from the 
configuration file — this way it seems to run fine (so far). But I assume it’s 
there for a reason so I’m not sure this is a solution at all...

Any help would be much appreciated!

Details:
1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) platform: CentOS release 6.8 (Final)
3) Operating system details (kernel name, release, version, etc.): Linux 
2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 
x86_64 GNU/Linux
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



trac-all.local-copy
Description: trac-all.local-copy
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] longitudinal tracula error

[Yendiki, Anastasia]

Hi Barbara - If you take out the "set baselist" part, you'll run the 
cross-sectional TRACULA stream, i.e., analyze each time point independently. So 
you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may 
not be used, but the files under the base template's directory are used. 
Longitudinal TRACULA maps between the base space to the space of each DWI time 
point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no 
official 6.0 version yet but multiple beta versions of it, it's hard to know 
which one you used.

Thanks,
a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira 
[barbara.avelar.pere...@ki.se]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] longitudinal tracula error

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

>From the mailing list, it seems a similar issue has been fixed in previous 
>updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, it asks for it: ERROR: 
cannot find /Documents/TRACULA/TEST/S0001.01

>From what I understand, the base is not necessary to run any analysis, but it 
>has to be there anyhow (?): 
>https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html 
>Maybe I am understanding this incorrectly?

Since the base is used to create the longitudinal output (*long*), including 
the aparc+aseg.mgz file, and those are then used in tracula, I thought I could 
run things without it. I decided to take out the “set baselist” part from the 
configuration file — this way it seems to run fine (so far). But I assume it’s 
there for a reason so I’m not sure this is a solution at all...

Any help would be much appreciated!

Details:
1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) platform: CentOS release 6.8 (Final)
3) Operating system details (kernel name, release, version, etc.): Linux 
2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 
x86_64 GNU/Linux
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] longitudinal tracula error

[Bárbara Avelar Pereira]

Dear FreeSurfer experts,

I’m running tracula on longitudinal data but I’ve encountered the following 
error at the “trac-all -prep” stage:  ERROR: flag ; unrecognized (see below)

trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c 
/Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd 
/Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ;
ERROR: flag ; unrecognized

As an example, I defined the parameters in my dmrirc file as:
set subjlist = ( S0001.01_T1 \
   S0001.01_T2 \
   S0004.00_T1 \
   S0004.00_T2 )

set baselist = ( S0001.01 \
S0001.01 \
S0004.00 \
S0004.00 )

set dcmlist =  ( S0001.01_T1/DTI.nii \
S0001.01_T2/DTI.nii \
S0004.00_T1/DTI.nii \
S0004.00_T2/DTI.nii )

From the mailing list, it seems a similar issue has been fixed in previous 
updates but I have tried both version 5.3 and 6.0 and still get this error...

My tracula directory contains 3 directories per participant: 2 with the 
*.long.* output for timepoint 1 and 2, and a directory with the base. Including 
the base gives the error above, but if I take it out, it asks for it: ERROR: 
cannot find /Documents/TRACULA/TEST/S0001.01

From what I understand, the base is not necessary to run any analysis, but it 
has to be there anyhow (?): 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html Maybe 
I am understanding this incorrectly?

Since the base is used to create the longitudinal output (*long*), including 
the aparc+aseg.mgz file, and those are then used in tracula, I thought I could 
run things without it. I decided to take out the “set baselist” part from the 
configuration file — this way it seems to run fine (so far). But I assume it’s 
there for a reason so I’m not sure this is a solution at all...

Any help would be much appreciated!

Details:
1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) platform: CentOS release 6.8 (Final)
3) Operating system details (kernel name, release, version, etc.): Linux 
2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 
x86_64 GNU/Linux
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Re: [Freesurfer] Longitudinal TRACULA: mri_convert

[Vincent Koppelmans]

Dear Anastasia,

I emailed with Dr. Knut Jørgen Bjuland because he had a similar issue 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg39745.html). 
He mentioned that obtaining a new license could solve the issue. It did, 
so my problem is resolved.

Best,

Vincent




Dear Anastasia,

I have checked the image and it looks good. I don't think the image is
the problem, especially considering that my issue is also popping up
with standard data. See for example the following code:


$ echo $FREESURFER_HOME
/home/mriuser/privatemodules/freesurfer

$ cksum $(which mri_convert)
1305133180 29171478 /home/mriuser/privatemodules/freesurfer/bin/mri_convert

$ echo $FSLDIR
/home/mriuser/privatemodules/fsl

$ mri_convert ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz test.mgh
mri_convert
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz
test.mgh
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz...
crypt_gkey = (null)
Segmentation fault (core dumped)




The reason I am posting this with 'Longitudinal TRACULA' in the title is
because I only have this issue with the mri_convert that is bundled with
the TRACULA update (see my first post). The original mri_convert bundled
with the centOS6 64bit version of FS 5.3.0 (stable) does let me convert
files. However, this version does not allow multiple frame numbers:

Original frame options of mri_convert (FS v5.3.0 stable centos6 64)
  -f,  --frame frameno
  keep only 0-based frame number

Frame options of the updated mri_convert
(tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz)
  -f,  --frame frameno [...]
  keep only 0-based frame number(s)

Longitudinal TRACULA pushes multiple files as arguments to 'mri_convert
--frame', which is why I need the updated version.

Do you have any suggestions for me?

Thank you!

best,

Vincent




Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA
but
probably something about the format of your input nifti volume. How did you
create that volume? Can you open it in freeview and view it normally?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert

Hello Freesurfer experts,

I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:



#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux



Some information about my setup:

*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz

*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64



Is there a fix for this problem?

Thanks!

- Vincent

___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Longitudinal TRACULA: mri_convert

[Vincent Koppelmans]

Dear Anastasia,

I have checked the image and it looks good. I don't think the image is 
the problem, especially considering that my issue is also popping up 
with standard data. See for example the following code:


$ echo $FREESURFER_HOME
/home/mriuser/privatemodules/freesurfer

$ cksum $(which mri_convert)
1305133180 29171478 /home/mriuser/privatemodules/freesurfer/bin/mri_convert

$ echo $FSLDIR
/home/mriuser/privatemodules/fsl

$ mri_convert ${FSLDIR}/data/standard/MNI152_T1_1mm.nii.gz test.mgh
mri_convert 
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz 
test.mgh
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from 
/home/mriuser/privatemodules/fsl/data/standard/MNI152_T1_1mm.nii.gz...
crypt_gkey = (null)
Segmentation fault (core dumped)




The reason I am posting this with 'Longitudinal TRACULA' in the title is 
because I only have this issue with the mri_convert that is bundled with 
the TRACULA update (see my first post). The original mri_convert bundled 
with the centOS6 64bit version of FS 5.3.0 (stable) does let me convert 
files. However, this version does not allow multiple frame numbers:

Original frame options of mri_convert (FS v5.3.0 stable centos6 64)
 -f,  --frame frameno
 keep only 0-based frame number

Frame options of the updated mri_convert 
(tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz)
 -f,  --frame frameno [...]
 keep only 0-based frame number(s)

Longitudinal TRACULA pushes multiple files as arguments to 'mri_convert 
--frame', which is why I need the updated version.

Do you have any suggestions for me?

Thank you!

best,

Vincent




Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA 
but
probably something about the format of your input nifti volume. How did you
create that volume? Can you open it in freeview and view it normally?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert

Hello Freesurfer experts,

I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:



#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux



Some information about my setup:

*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz

*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64



Is there a fix for this problem?

Thanks!

- Vincent
___
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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Longitudinal TRACULA: mri_convert

[Yendiki, Anastasia]

Hi Vincent - Looks like an mri_convert error, so not specific to TRACULA but 
probably something about the format of your input nifti volume. How did you 
create that volume? Can you open it in freeview and view it normally?


a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Vincent Koppelmans 
[vkop...@umich.edu]
Sent: Wednesday, November 30, 2016 1:33 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Longitudinal TRACULA: mri_convert

Hello Freesurfer experts,

I am trying to run longitudinal TRACULA but I am getting an error early
on in the process that seems to originate from mri_convert:



#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux



Some information about my setup:

*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz

*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64



Is there a fix for this problem?

Thanks!

- Vincent

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Longitudinal TRACULA: mri_convert

[Vincent Koppelmans]

Hello Freesurfer experts,

I am trying to run longitudinal TRACULA but I am getting an error early 
on in the process that seems to originate from mri_convert:



#-
/home/mriuser/privatemodules/freesurfer/bin/trac-preproc
#-
#@# Image corrections Wed Nov 30 09:10:55 EST 2016
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz 
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
mri_convert /datapath/2171/01_Raw_Data/DWI/2171_02_DWI.nii.gz 
/datapath/2171/04_TRACULA/2171_02.long.2171_T/dmri/dwi_orig.nii.gz
Segmentation fault (core dumped)
Linux 3.10.0-327.4.4.el7.x86_64 #1 SMP Tue Jan 5 16:07:00 UTC 2016 
x86_64 x86_64 x86_64 GNU/Linux



Some information about my setup:

*Freesurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

*Freesurfer TRACULA update installed:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-tracula-addons/tracula.update.centos6_x86_64.5.3.2014_05_26.tar.gz

*Linux version:
CentOS Linux release 7.2.1511 (Core)
centos-release-7-2.1511.el7.centos.2.10.x86_64



Is there a fix for this problem?

Thanks!

- Vincent

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] longitudinal tracula

[Anastasia Yendiki]

Hi Michael - There is no bvec file associated with the base template. The 
base template is a structural (the median of a subject's structural time 
points) and not a diffusion scan.


The way you'd want to account for different amounts of motion across 
subjects in a cross-sectional analysis, you'd probably want to account for 
different changes in motion in a longitudinal study. Whether you'd also 
want to discard data is an open question.


a.y

On Mon, 4 Jul 2016, Harms, Michael wrote:



So, what bvec/bvec file should be associated with the BASE scan?  It isn’t
clear to me how the bvec/bval in the BASE scan get used in trac-paths.

I see the point of your note of caution, but unless someone moved the same
amount (and for the same frames) for their sessions in a longitudinal
study, the same issue applies, even if you use all frames “as is”.  In
that case, the potential bias would be due to using data of differing
quality across sessions.  In a sense, we are just making the issue
explicit by discarding bad frames as part of a QC step.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/4/16, 2:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:


Hi Michael - Indeed it should not be too difficult to add the feature of
specifying the b-value table for each scan and I can add this in the next
version.

However, I would be a bit careful with removing different DWI volumes for
different time points. The acquisition should be as consistent as possible
across time points. If you find that there's a longitudinal change, would
this be because there were different directions/b-values in each time
point or because of an actual change in the brain? I suppose that, unless
there's a systematic bias, you might expect that these changes will be in
different directions for different subjects and would then average out.
But it's a tricky issue.

Best,
a.y

On Fri, 1 Jul 2016, Harms, Michael wrote:



Hi Anastasia,
Looking through the trac-preproc and trac-paths scripts, it is now clear
to me that all the time points for a given subject have to be
contained/specified
within the same dmrirc configuration file in order to implement a
longitudinal TRACULA analysis.  So, I've answered my previous question in
that regard.

The challenge in our case is that we have separately pre-processed the
dMRI data for each subject and time point, removing bad frames/volumes
(using the
DTIPrep QA tool).  Thus, the bvecs/bvals are not identical for all the
time points of a given subject.  We can specify the bvec file for each
subject/time
point using the bveclist configuration parameter.  But there is no
analog available for bvals, since only a single bvalfile can be
specified.

I see that this issue has been raised in a couple other posts relatively
recently (2015):
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html
but no working solution was provided at that time.

I’m wondering if there is perhaps now a development version of TRACULA
that supports a “bvallist” capability?  If not, it doesn’t look like it
would be too
difficult to modify trac-all  to include that capability (modeling after
what is already in trac-all for the bveclist/bvecfile stuff).  But, in
that case,
it isn’t immediately clear to me if there are other downstream “gotchas”
in the preproc, paths, or stats stage specific scripts/binaries that
would need
modifications as well.  [I don’t see anything in the sections related to
the BASE-specific processing in trac-preproc involving bvals/bvecs, so
think we are
fine there.  But it is harder for me to tell what is going on in
trac-paths].

thanks,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Harms,
Michael" <mha...@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, June 29, 2016 at 5:00 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula


Hi,
When running TRACULA with longitudinal data, is it necessary for all
scan waves of a given subject to be included in a single dmrirc file?  My
initial
thought was “no”, that it would be fine to run one scan wave per subject
per dmrirc file (as lo

Re: [Freesurfer] longitudinal tracula

[Harms, Michael]

So, what bvec/bvec file should be associated with the BASE scan?  It isn’t
clear to me how the bvec/bval in the BASE scan get used in trac-paths.

I see the point of your note of caution, but unless someone moved the same
amount (and for the same frames) for their sessions in a longitudinal
study, the same issue applies, even if you use all frames “as is”.  In
that case, the potential bias would be due to using data of differing
quality across sessions.  In a sense, we are just making the issue
explicit by discarding bad frames as part of a QC step.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 7/4/16, 2:41 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki" <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
ayend...@nmr.mgh.harvard.edu> wrote:


Hi Michael - Indeed it should not be too difficult to add the feature of
specifying the b-value table for each scan and I can add this in the next
version.

However, I would be a bit careful with removing different DWI volumes for
different time points. The acquisition should be as consistent as possible
across time points. If you find that there's a longitudinal change, would
this be because there were different directions/b-values in each time
point or because of an actual change in the brain? I suppose that, unless
there's a systematic bias, you might expect that these changes will be in
different directions for different subjects and would then average out.
But it's a tricky issue.

Best,
a.y

On Fri, 1 Jul 2016, Harms, Michael wrote:

>
> Hi Anastasia,
> Looking through the trac-preproc and trac-paths scripts, it is now clear
>to me that all the time points for a given subject have to be
>contained/specified
> within the same dmrirc configuration file in order to implement a
>longitudinal TRACULA analysis.  So, I've answered my previous question in
>that regard.
>
> The challenge in our case is that we have separately pre-processed the
>dMRI data for each subject and time point, removing bad frames/volumes
>(using the
> DTIPrep QA tool).  Thus, the bvecs/bvals are not identical for all the
>time points of a given subject.  We can specify the bvec file for each
>subject/time
> point using the bveclist configuration parameter.  But there is no
>analog available for bvals, since only a single bvalfile can be
>specified.
>
> I see that this issue has been raised in a couple other posts relatively
>recently (2015):
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html
> but no working solution was provided at that time.
>
> I’m wondering if there is perhaps now a development version of TRACULA
>that supports a “bvallist” capability?  If not, it doesn’t look like it
>would be too
> difficult to modify trac-all  to include that capability (modeling after
>what is already in trac-all for the bveclist/bvecfile stuff).  But, in
>that case,
> it isn’t immediately clear to me if there are other downstream “gotchas”
>in the preproc, paths, or stats stage specific scripts/binaries that
>would need
> modifications as well.  [I don’t see anything in the sections related to
>the BASE-specific processing in trac-preproc involving bvals/bvecs, so
>think we are
> fine there.  But it is harder for me to tell what is going on in
>trac-paths].
>
> thanks,
> -MH
>
> --
> Michael Harms, Ph.D.
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave. Tel: 314-747-6173
> St. Louis, MO  63110 Email: mha...@wustl.edu
>
> From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Harms,
>Michael" <mha...@wustl.edu>
> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Date: Wednesday, June 29, 2016 at 5:00 PM
> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: [Freesurfer] longitudinal tracula
>
>
> Hi,
> When running TRACULA with longitudinal data, is it necessary for all
>scan waves of a given subject to be included in a single dmrirc file?  My
>initial
> thought was “no”, that it would be fine to run one scan wave per subject
>per dmrirc file (as long as the “baselist” variable is set appropriately
>for each
> scan wave and subject).
>
> But looking at the ‘trac-all’ script, I see
>
> if ($#baselist == 0) then#--->>> A sing

Re: [Freesurfer] longitudinal tracula

[Anastasia Yendiki]

Hi Michael - Indeed it should not be too difficult to add the feature of 
specifying the b-value table for each scan and I can add this in the next 
version.


However, I would be a bit careful with removing different DWI volumes for 
different time points. The acquisition should be as consistent as possible 
across time points. If you find that there's a longitudinal change, would 
this be because there were different directions/b-values in each time 
point or because of an actual change in the brain? I suppose that, unless 
there's a systematic bias, you might expect that these changes will be in 
different directions for different subjects and would then average out. 
But it's a tricky issue.


Best,
a.y

On Fri, 1 Jul 2016, Harms, Michael wrote:



Hi Anastasia,
Looking through the trac-preproc and trac-paths scripts, it is now clear to me 
that all the time points for a given subject have to be contained/specified
within the same dmrirc configuration file in order to implement a longitudinal 
TRACULA analysis.  So, I've answered my previous question in that regard.

The challenge in our case is that we have separately pre-processed the dMRI 
data for each subject and time point, removing bad frames/volumes (using the
DTIPrep QA tool).  Thus, the bvecs/bvals are not identical for all the time 
points of a given subject.  We can specify the bvec file for each subject/time
point using the bveclist configuration parameter.  But there is no analog 
available for bvals, since only a single bvalfile can be specified.  

I see that this issue has been raised in a couple other posts relatively 
recently (2015):
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html
but no working solution was provided at that time.

I’m wondering if there is perhaps now a development version of TRACULA that 
supports a “bvallist” capability?  If not, it doesn’t look like it would be too
difficult to modify trac-all  to include that capability (modeling after what 
is already in trac-all for the bveclist/bvecfile stuff).  But, in that case,
it isn’t immediately clear to me if there are other downstream “gotchas” in the 
preproc, paths, or stats stage specific scripts/binaries that would need
modifications as well.  [I don’t see anything in the sections related to the 
BASE-specific processing in trac-preproc involving bvals/bvecs, so think we are
fine there.  But it is harder for me to tell what is going on in trac-paths].

thanks,
-MH

-- 
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Harms, Michael" 
<mha...@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, June 29, 2016 at 5:00 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula


Hi,
When running TRACULA with longitudinal data, is it necessary for all scan waves 
of a given subject to be included in a single dmrirc file?  My initial
thought was “no”, that it would be fine to run one scan wave per subject per 
dmrirc file (as long as the “baselist” variable is set appropriately for each
scan wave and subject).

But looking at the ‘trac-all’ script, I see

if ($#baselist == 0) then#--->>> A single time point for each subject
…
else#--->>> Multiple time points for each subject
…

So, I’m wondering why different sections in the code would be necessary if in 
fact it is ok to process a single scan wave per dmrirc file.

thanks,
-MH

-- 
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu

 





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

 





The materials in this message are priva

Re: [Freesurfer] longitudinal tracula

[Harms, Michael]

Hi Anastasia,
Looking through the
trac-preproc and
trac-paths scripts, it is now clear to me that all the time points for a given subject have to be contained/specified
 within the same dmrirc configuration file in order to implement a longitudinal TRACULA analysis.  So, I've answered my previous question in that regard.




The challenge in our case is that we have separately pre-processed the dMRI data for each subject and time point, removing bad frames/volumes (using the DTIPrep QA tool).
  Thus, the bvecs/bvals are not identical for all the time points of a given subject.  We can specify the bvec file for each subject/time point using the
bveclist configuration parameter.  But there is no analog available for bvals, since only a single
bvalfile can be specified.  




I see that this issue has been raised in a couple other posts relatively recently (2015):

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html

but no working solution was provided at that time.



I’m wondering if there is perhaps now a development version of TRACULA that supports a “bvallist”
 capability?  If not, it doesn’t look like it would be too difficult to modify 
trac-all  to include that capability (modeling after what is already
 in trac-all for the
bveclist/bvecfile
stuff).  But, in that case, it isn’t immediately clear to me if there are other downstream “gotchas” in the preproc, paths, or stats stage specific scripts/binaries
 that would need modifications as well.  [I don’t see anything in the sections related to the BASE-specific processing in
trac-preproc involving bvals/bvecs, so think we are fine there.  But it is harder for me to tell what is going on in
trac-paths].




thanks,

-MH





-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu








From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Harms, Michael" <mha...@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, June 29, 2016 at 5:00 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula







Hi,
When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file?  My initial thought was “no”, that it would be fine to run one scan wave
 per subject per dmrirc file (as long as the “baselist” variable is set appropriately for each scan wave and subject).


But looking at the ‘trac-all’ script, I see


if ($#baselist == 0) then#--->>> A single time point for each subject
…
else#--->>> Multiple time points for each subject
…


So, I’m wondering why different sections in the code would be necessary if in fact it is ok to process a single scan wave per dmrirc file.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu




 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.





 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


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[Freesurfer] longitudinal tracula

[Harms, Michael]

Hi,
When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file?  My initial thought was “no”, that it would be fine to run one scan wave
 per subject per dmrirc file (as long as the “baselist” variable is set appropriately for each scan wave and subject).


But looking at the ‘trac-all’ script, I see


if ($#baselist == 0) then
#--->>> A single time point for each subject
…
else
#--->>> Multiple time points for each subject
…


So, I’m wondering why different sections in the code would be necessary if in fact it is ok to process a single scan wave per dmrirc file.


thanks,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu




 



The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended
 recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone
 or return mail.


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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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Re: [Freesurfer] Longitudinal TRACULA - Error in path reconstruction

[Anastasia Yendiki]

Hi Emad - I believe that it's not finding your freesurfer recons. They 
should be under the $SUBJECTS_DIR and have the same names for time points 
and longitudinal template as what is under your tracula output directory 
(if the latter is different from SUBJECTS_DIR).


Best,
a.y

On Fri, 1 Apr 2016, Emad Ahmadi wrote:


Hi Anastasia,

I’ve attached the log files. The cases are:

1. Case #2; time points: 2a, 2b; base template: 2tem
2. Case #3; time points: 3a, 3b; base template: 3tem

Thank you again for your help,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu



On Apr 1, 2016, at 10:49 AM, Anastasia Yendiki  
wrote:


Hi Emad - The error happens at the very beginning, so I'm wondering if 
something went wrong in the previous steps, before -path. Can you please send 
me the entire trac-all.log of one of your subjects? Thank you!

a.y

On Wed, 30 Mar 2016, Emad Ahmadi wrote:


Hi Anastasia,

I hope you’re enjoying your evening!

I’m doing longitudinal TRACULA analysis on two subjects, each having two time 
points. I have already taken the steps of longitudinal recon-all and trac-all -prep 
& -bedp.

Now I’m trying to do trac-all -path, but it gives me an error that I cannot 
recognize. I would greatly appreciate your help. I’ve attached the log files 
and the config file.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Longitudinal TRACULA - Error in path reconstruction

[Anastasia Yendiki]

Hi Emad - The error happens at the very beginning, so I'm wondering if 
something went wrong in the previous steps, before -path. Can you please 
send me the entire trac-all.log of one of your subjects? Thank you!


a.y

On Wed, 30 Mar 2016, Emad Ahmadi wrote:


Hi Anastasia,

I hope you’re enjoying your evening!

I’m doing longitudinal TRACULA analysis on two subjects, each having two time 
points. I have already taken the steps of longitudinal recon-all and trac-all -prep 
& -bedp.

Now I’m trying to do trac-all -path, but it gives me an error that I cannot 
recognize. I would greatly appreciate your help. I’ve attached the log files 
and the config file.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Longitudinal TRACULA - Error in path reconstruction

[Emad Ahmadi]

Hi Anastasia,

I hope you’re enjoying your evening!

I’m doing longitudinal TRACULA analysis on two subjects, each having two time 
points. I have already taken the steps of longitudinal recon-all and trac-all 
-prep & -bedp.

Now I’m trying to do trac-all -path, but it gives me an error that I cannot 
recognize. I would greatly appreciate your help. I’ve attached the log files 
and the config file.

Thank you so much,
Emad


Emad Ahmadi, MD
---
Research Fellow in Radiology
Massachusetts General Hospital
Harvard Medical School

25 New Chardon Street, Suite 400
Boston, MA 02114
Tel: 617 726 5237
Email: e...@nmr.mgh.harvard.edu


trc_.e11258806
Description: application/applefile


trc_.o11258806
Description: Binary data


trc_0001.e11258808
Description: application/applefile


trc_0001.o11258808
Description: Binary data
# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
#_
setenv SUBJECTS_DIR /cluster/guptagp/Emad/3LT/subjDir
setenv RAW_DATA /cluster/guptagp/Emad/3LT/rawData
#_

# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
#set dtroot = /path/to/tracts/of/ducks

# Subject IDs (one per time point per subject)
#_
set subjlist = ( 2a \
 2b \
 3a \
 3b )
#_

# Longitudinal base template subject IDs (one for each time point above)
#_
set baselist = ( 2tem \
 2tem \
 3tem \
 3tem )
#_

# 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 the gradient table and b-value table must be specified (see below)
#_
set dcmroot = $RAW_DATA
set dcmlist = ( 2a/Diffusion/IM-0001-0001.dcm \
2b/Diffusion/IM-0001-0001.dcm \
3a/Diffusion/IM-0001-0001.dcm \
3b/Diffusion/IM-0003-0001.dcm )
#_

# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if inputs are not MGH DICOMs
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#_
set bveclist = (/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt \
/cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt)
#_

# Diffusion gradient table (if using the same one for all scans)
# Must be specified if inputs are not MGH DICOMs
# The table must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#_
#set bvecfile = /cluster/guptagp/Emad/3LT/subjDir/codes/bvecXinv.txt
#_

# Diffusion b-value table
# Must be specified if inputs are not MGH DICOMs
# There must be as many b-values as volumes in the diffusion data set
# Default: Read from DICOM header
#_
set bvalfile = /cluster/guptagp/Emad/3LT/subjDir/codes/bval.txt
#_

# Perform registration-based B0-inhomogeneity compensation?
# Default: 0 (no)
#
#set dob0 = 1

# Input B0 field map magnitude DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
#set b0mlist = ( huey/year1/fmag/XXX-1.dcm \
huey/year2/fmag/XXX-1.dcm \
dewey/year1/fmag/XXX-1.dcm \
dewey/year2/fmag/XXX-1.dcm \
louie/year1/fmag/XXX-1.dcm \
louie/year2/fmag/XXX-1.dcm )

# Input B0 field map phase DICOMs (file names relative to dcmroot)
# Only used if dob0 = 1
# Default: None
#
#set b0plist = ( huey/year1/fphas/XXX-1.dcm \
huey/year2/fphas/XXX-1.dcm \
dewey/year1/fphas/XXX-1.dcm \
dewey/year2/fphas/XXX-1.dcm \
louie/year1/fphas/XXX-1.dcm \
   

Re: [Freesurfer] longitudinal tracula error

[Anastasia Yendiki]

Hi Francesco - Please attach your dmrirc, and also the tracula log file of 
your subject (scripts/trac-all.log). It's hard to guess what went wrong 
without looking at the complete output.


Thanks,
a.y

On Thu, 29 Jan 2015, Francesco Siciliano wrote:


Hi,
I have been unsuccessful in getting longitudinal tracula to run. I have been 
directing my dmrirc file to skip the registration-based B0-inhomogeneity 
compensation (by setting it to 0).
However, when I try to run trac-all prep, I get an error message asking to 
specify a field map for each input. I also tried running the step and 
specifying appropriate field maps, yet
still got the same error. Any help with this would be appreciated.

Best,


Francesco Siciliano, B.A. Research Assistant
Department of Child and Adolescent Psychiatry
The New York State Psychiatric Institute
Columbia University
1051 Riverside Drive, Unit 74
New York, NY 10032
(646) 774-5703

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] longitudinal tracula error

[Francesco Siciliano]

Hi,

I have been unsuccessful in getting longitudinal tracula to run. I have been 
directing my dmrirc file to skip the registration-based B0-inhomogeneity 
compensation (by setting it to 0). However, when I try to run trac-all prep, I 
get an error message asking to specify a field map for each input. I also tried 
running the step and specifying appropriate field maps, yet still got the same 
error. Any help with this would be appreciated.

Best,


Francesco Siciliano, B.A.
Research Assistant
Department of Child and Adolescent Psychiatry
The New York State Psychiatric Institute
Columbia University
1051 Riverside Drive, Unit 74
New York, NY 10032
(646) 774-5703
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