date:20210609

Re: [Freesurfer] mri_hippocampal-subfields error: MATLAB exited for no reason (Iglesias Gonzalez, Juan E.) Re: Freesurfer Digest, Vol 208, Issue 17

2021-06-09 Thread 林鈺庭

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Dear Developer and Eugenio,

Thank you for the suggestion! I tried to cd into FreeSurfer root or the
specific folder which contains the data (i.e.,
/usr/local/freesurfer/subjects/S013 or /usr/local/freesurfer/subjects), and
also tried to make the optional argument to override the subjects directory
(i.e., /usr/local/freesurfer/subjects/S013
or /usr/local/freesurfer/subjects)

However, even doing so, there's still no .txt file to be written since
couldn't find it in any of the folders. ( we applied the 'find' command,
too) Could you way in any more suggestions? Thank you in advance!

Here're the terminal commands:




















































































*[root@d7d0454589af S013]# quantifyHAsubregions.sh hippoSf T1
results013.txtGathering results from subjects in:
 /usr/local/freesurfer/subjectsUsing the prefix name:   hippoSfUsing the
suffix name:   T1And writing them to:   results013.txt[root@d7d0454589af
S013]# cd ..[root@d7d0454589af subjects]# ls -ltotal 12316-rw-rw-r--  1
root root1512 Jul 23  2020 READMEdrwx--S--- 11 root root4096 Jun  7
06:32 S013drwxrwsr-x  6 root root4096 Nov 11  2008 V1_averagedrwxrwsr-x
10 root root4096 Jul 23  2020 bertdrwxrwsr-x 12 root root4096 Mar
13  2012 cvs_avg35drwxrwsr-x 13 root root4096 Apr 14  2015
cvs_avg35_inMNI152drwxrwsr-x  8 root root4096 Nov 13  2015
fsaveragedrwxrwsr-x  8 root root4096 Sep 22  2009 fsaverage3drwxrwsr-x
 8 root root4096 Sep 22  2009 fsaverage4drwxrwsr-x  8 root root4096
May 31  2011 fsaverage5drwxrwsr-x  8 root root4096 Sep 22  2009
fsaverage6drwxrwsr-x 12 root root4096 Aug 20  2012
fsaverage_symdrwxrwsr-x  6 root root4096 Mar 30  2010
lh.EC_averagedrwxrwsr-x  6 root root4096 Mar 30  2010
rh.EC_average-rw-rw-r--  1 root root 6280209 Jul 23  2020
sample-001.mgz-rw-rw-r--  1 root root 6269785 Jul 23  2020
sample-002.mgz[root@d7d0454589af subjects]# cd S013[root@d7d0454589af
S013]# quantifyHAsubregions.sh hippoSf T1 results013.txt
/usr/local/freesurfer/subjects/S013Gathering results from subjects in:
 /usr/local/freesurfer/subjects/S013Using the prefix name:   hippoSfUsing
the suffix name:   T1And writing them to:
 results013.txt[root@d7d0454589af S013]# cd ..[root@d7d0454589af subjects]#
ls -ltotal 12316-rw-rw-r--  1 root root1512 Jul 23  2020
READMEdrwx--S--- 11 root root4096 Jun  7 06:32 S013drwxrwsr-x  6 root
root4096 Nov 11  2008 V1_averagedrwxrwsr-x 10 root root4096 Jul 23
 2020 bertdrwxrwsr-x 12 root root4096 Mar 13  2012 cvs_avg35drwxrwsr-x
13 root root4096 Apr 14  2015 cvs_avg35_inMNI152drwxrwsr-x  8 root root
   4096 Nov 13  2015 fsaveragedrwxrwsr-x  8 root root4096 Sep 22  2009
fsaverage3drwxrwsr-x  8 root root4096 Sep 22  2009 fsaverage4drwxrwsr-x
 8 root root4096 May 31  2011 fsaverage5drwxrwsr-x  8 root root4096
Sep 22  2009 fsaverage6drwxrwsr-x 12 root root4096 Aug 20  2012
fsaverage_symdrwxrwsr-x  6 root root4096 Mar 30  2010
lh.EC_averagedrwxrwsr-x  6 root root4096 Mar 30  2010
rh.EC_average-rw-rw-r--  1 root root 6280209 Jul 23  2020
sample-001.mgz-rw-rw-r--  1 root root 6269785 Jul 23  2020
sample-002.mgz[root@d7d0454589af subjects]# quantifyHAsubregions.sh hippoSf
T1 results013.txtGathering results from subjects in:
 /usr/local/freesurfer/subjectsUsing the prefix name:   hippoSfUsing the
suffix name:   T1And writing them to:   results013.txt[root@d7d0454589af
subjects]# ls -ltotal 12316-rw-rw-r--  1 root root1512 Jul 23  2020
READMEdrwx--S--- 11 root root4096 Jun  7 06:32 S013drwxrwsr-x  6 root
root4096 Nov 11  2008 V1_averagedrwxrwsr-x 10 root root4096 Jul 23
 2020 bertdrwxrwsr-x 12 root root4096 Mar 13  2012 cvs_avg35drwxrwsr-x
13 root root4096 Apr 14  2015 cvs_avg35_inMNI152drwxrwsr-x  8 root root
   4096 Nov 13  2015 fsaveragedrwxrwsr-x  8 root root4096 Sep 22  2009
fsaverage3drwxrwsr-x  8 root root4096 Sep 22  2009 fsaverage4drwxrwsr-x
 8 root root4096 May 31  2011 fsaverage5drwxrwsr-x  8 root root4096
Sep 22  2009 fsaverage6drwxrwsr-x 12 root root4096 Aug 20  2012
fsaverage_symdrwxrwsr-x  6 root root4096 Mar 30  2010
lh.EC_averagedrwxrwsr-x  6 root root4096 Mar 30  2010
rh.EC_average-rw-rw-r--  1 root root 6280209 Jul 23  2020
sample-001.mgz-rw-rw-r--  1 root root 6269785 Jul 23  2020 sample-002.mgz*

Best regards,
Josephine
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[Freesurfer] Fw: Problem when using freesurfer

2021-06-09 Thread Yuqian Chen

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Dear Sir or Madam,
Hope you are doing well! Thank you very much for your contribution to the 
freesurfer software which offers great help to research in the neuroimaging 
area. However, I met a problem when using it and I hope you can help me with it.
The freesurfer version I use is freesurfer-linux-centos7_x86_64-7.1.1.tar.gz. I 
hope to implement AnatomiCuts with my own data which is tractography data 
(.vtk) reconstructed from HCP dataset with ukf tractography method. When I 
tried to run the dmri_AnatomiCuts command (the complete command is: 
dmri_AnatomiCuts -s wmparc.nii.gz -f 100307_ukf_pp.vtk -c 100 -n 14 -e 50 -o 
output -d s), the following messages appears:

 ups
 ups
 ups
 ups
 ups
 ups
...
 queue emplace 3894
 queue emplace 0


It seems that the algorithm is running. But it just stays here and I cannot get 
the final results even with input data of only 100 fibers divided into 2 
clusters. I am really confused what is going on here. Are there any special 
requirements for the input data?
Your help will be greatly appreciated.

Regards,
Yuqian

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[Freesurfer] Samseg pallidum issue

2021-06-09 Thread Russo, Andrew William

Hello FreeSurfer Developers,

I ran longitudinal samseg on a group of subjects with MS (each with 5 MRI 
timepoints over 2 years) and found that the average volume of the pallidum 
increased over time, while other subcortical volumes (caudate, putamen, 
thalamus) decreased. I also tried longitudinal samseg using the 
--pallidum-separate flag and had similar results. As the putamen gets smaller 
it looks like the pallidum volume grows to fill in the space. Have you 
encountered this issue before?

I am using enhanced T1 images (made from T1, FLAIR, and FA data) as the input 
for run_samseg_long (FreeSurfer v7).

Thank you,
Andrew

Andrew Russo
Clinical Research Coordinator
Multiple Sclerosis Imaging Lab
Massachusetts General Hospital
149 13th Street | Boston, MA 02129
617-726-7531
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[Freesurfer] mri_glmfit with pvr

2021-06-09 Thread stdp82

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Thanks

If I have 4 groups

GroupDescriptorFile 1
Title XXX
Class G1
Class G2
Class G3
Class G4

Input subj1 G1

Input subj2 G3

Input subj3 G2

Input subj4 G2

Input subj5 G4




Are the contrasts below corrected?

G1_only_thick 1 0 0 0

G2_only_thick 1 0 0 0

G3_only_thick 1 0 0 0

G4_only_thick 1 0 0 0

G1+G2-G3+G4_thick 0.5 0.5 -0.5 -0.5

G3+G4+G2+G1_thick -0.5 -0.5 0.5 0.5

G1+G2+G3+G4_thick 0.25 0.25 0.25 0.25

Thanks

Stefano



Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See, example, 
this thread 
https://secure-web.cisco.com/1AQW2Zmfaui0gjHDqfC-62qKrikS49RYbR7pNeQeTr2onenw4VdfUzxAD-yIGZ-RWjvqJqELbkeBxh-eEoHsrsM5sjWYXowa55h5HmDwS2HP-LGyy4SFdxgEGV4R5lhBK0pMIf8VhbvlMkoZpaRCGO9sEsN89fc0rgzYL83HiJvCE6vviDul0-oFKliOXHXlXxdd6kqkmidKljGOb8tcDOZX_cjdrLsH7G0YoQYuiemfio9U_qVDhfkyDU2t5DWXRvlVbn_e9Nkc3DJ7h0XjhCA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg18790.htmlOn
 6/3/2021 10:22 AM, std...@virgilio.it wrote:

> External Email - Use Caution Hi, how can I perform vertex by vertex (surface) 
> analysis of covariance between functional connectivity data (FS-FAST) and 
> cortical thickness, regressing out the effect of groups?My mean concern is 
> how buid the fsgd file. Stefano
> 

Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM, "Douglas N Greve" 
 wrote:

>Hi Aga, what you have done is correct, no need to include the pvr in the
>fsgd.
>doug
>
>Burzynska, Aga wrote:
>> Dear all,
>> I am trying to make group level analysis of functional data on the
>>surface and add per-vertex regressors (PVR, here: cortical thickness)
>>into the design. When I view the results I have the feeling that the PVR
>>is not really included in the model:
>>
>> I am using the command:
>> mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd
>>Group1versusGroup2.fsgd  --pvr lh.thickness.10.mgh --C
>>Group1only_thickness.mat --C Group2only_thickness.mat --C
>>Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C
>>Group1plusGroup2_thickness.mat
>>
>> where
>> cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed
>>level analysis (combining the runs) for each participant
>> fsgd file contains:
>> GroupDescriptorFile 1
>> Title Group1versusGroup2
>> Class Group1 
>> Class Group2
>> Input 1109 Group1
>> Input 1110 Group1
>> Input  Group1
>> Input 1112 Group1
>> ...
>> Input 2280  Group2
>> Input 2282  Group2
>> Input 2283  Group2
>> Input 2284  Group2
>>
>> The PVR is a file containing thickness maps for each participant,
>>concatenated in the same order as for the functional data.
>>
>> So there are 2 main regressors (1 factor, 2 levels), but the contrast
>>files contain 3 regressors (the third one is the PVE), for instance:
>> Group1minusGroup2_thickness.mat contains  1 -1 0.
>>
>> Does it look correct?
>> Should the pvr regressor be included in the fsdg file? How can I do it?
>>
>> Thank you very much for your help,
>> Cheers,
>> Aga
>>
>> ___
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>>
>>   
>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>
>
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[Freesurfer] LGI FS 7.1

2021-06-09 Thread Del Re, Elisabetta

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Dear FS team,
what are differences if any between LGI in FS 5.3 and 7.1?
Thank you so much,
best wishes,
Elisabetta
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[Freesurfer] Ill-Conditioned/Badly Scaled Matrix Error

2021-06-09 Thread Lurie, Lucy

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Hello

I am trying to a whole brain analysis with one group and five covariates. I am 
getting an error that the design matrix may be ill-conditioned or badly scaled. 
I checked over the fsgd file in TextEdit and it seems to be formatted 
correctly. I am using Freesurfer version 5.3.0 and my platform is macOS Big Sur 
version 11.4. I would appreciate any help further troubleshooting this error. 
Thank you!

ERROR: matrix is ill-conditioned or badly scaled, condno = 13065
Possible problem with experimental design: Check for duplicate entries and/or 
lack of range of continuous variables within a class. If you seek help with 
this problem, make sure to send:
1. Your command line: mri_glmfit --y 
lh.eig_cgORCE_baselineORCE_teenCG.thickness.10.mgh --fsgd 
eig_cgORCE_baselineORCE_teenCG.fsgd dods --C eig_cgORCE3042_slope.mtx --C 
eig_cgORCEbaseline_slope.mtx --C eig_teenCGqual_slope.mtx --surf fsaverage lh 
--cortex --glmdir lh.eig_cgORCE_baselineORCE_teenCGagesex.glmdir
2. The FSGD file (if using one)
3. And the design matrix

Design matrix --
1.000   0.000   16.660   2.950   2.200   0.000;
1.000   0.000   16.960   1.900   2.600   0.000;
1.000   0.000   17.390   2.450   2.800   0.000;
1.000   1.000   17.130   2.300   2.500   0.000;
1.000   1.000   16.980   2.400   2.300   0.000;
1.000   0.000   17.690   2.200   2.900   0.000;
1.000   1.000   16.870   2.750   2.900   1.000;
1.000   0.000   17.570   2.550   1.700   0.000;
1.000   0.000   17.130   2.150   1.928   0.000;
1.000   1.000   17.650   2.750   2.200   0.000;
1.000   1.000   17.210   2.450   2.500   1.000;
1.000   0.000   15.610   3.100   1.565   1.000;
1.000   0.000   16.440   2.650   2.300   0.000;
1.000   1.000   17.350   2.400   2.600   0.000;
1.000   0.000   16.800   1.600   1.400   0.000;
1.000   1.000   17.980   2.200   2.300   1.000;
1.000   1.000   16.890   2.800   1.600   1.000;
1.000   0.000   16.760   1.100   1.300   0.000;
1.000   1.000   16.790   2.500   1.400   0.000;
1.000   1.000   16.620   2.900   2.800   0.000;
1.000   1.000   16.500   2.500   1.200   0.000;
1.000   1.000   16.290   2.700   3.200   0.500;
1.000   0.000   16.440   3.100   2.500   1.000;
1.000   0.000   17.540   2.100   2.100   1.000;
1.000   1.000   16.810   1.900   2.600   1.000;
1.000   0.000   17.110   2.650   2.400   0.000;
1.000   1.000   16.520   2.000   2.300   0.000;
1.000   1.000   16.520   3.100   3.400   1.000;
1.000   0.000   16.320   3.300   2.800   0.500;
1.000   0.000   16.380   3.200   1.900   1.000;
1.000   0.000   16.570   2.800   2.000   0.000;
1.000   1.000   16.250   2.200   1.600   0.000;
1.000   1.000   16.820   2.900   2.600   1.000;
1.000   0.000   16.580   2.600   2.800   0.000;
1.000   1.000   16.730   2.850   3.150   0.000;
1.000   0.000   16.310   2.600   1.900   0.000;
1.000   1.000   17.010   1.700   2.400   0.000;
1.000   1.000   16.360   3.200   3.200   0.000;
1.000   1.000   16.490   2.400   1.525   0.000;
1.000   0.000   16.300   2.400   1.450   1.000;
1.000   0.000   16.060   2.200   1.300   0.000;
1.000   1.000   16.600   2.200   2.000   0.000;
1.000   0.000   16.720   3.300   2.500   0.000;
1.000   1.000   16.160   2.300   2.200   0.000;
1.000   1.000   16.140   2.800   1.850   0.000;
1.000   1.000   16.550   3.100   2.950   1.000;
1.000   1.000   17.300   3.450   2.700   1.000;
1.000   0.000   16.940   3.000   2.200   1.000;
1.000   1.000   16.550   2.700   2.850   0.000;
1.000   0.000   17.170   3.000   2.900   1.000;
1.000   0.000   17.150   2.800   2.450   0.000;
1.000   0.000   16.650   3.100   1.900   0.500;
1.000   0.000   16.070   2.700   2.900   1.000;
1.000   1.000   16.720   1.800   1.450   1.000;
1.000   0.000   16.150   2.900   1.000   0.000;
1.000   1.000   16.120   2.400   2.200   1.000;
1.000   1.000   17.540   2.600   2.600   0.000;
1.000   1.000   16.840   2.900   1.100   0.000;
1.000   1.000   15.790   3.100   1.600   1.000;
1.000   1.000   16.430   2.800   1.500   0.000;
1.000   0.000   16.390   3.300   2.700   1.000;
1.000   0.000   16.480   3.350   3.000   0.000;
1.000   1.000   16.930   3.000   1.000   0.000;
1.000   1.000   15.550   2.200   2.600   0.000;
1.000   1.000   17.080   2.900   1.500   0.000;
1.000   0.000   16.850   2.500   2.200   0.500;
1.000   1.000   16.700   2.200   1.800   0.000;
1.000   1.000   15.930   2.600   2.000   1.000;
1.000   1.000   16.080   2.600   1.200   0.500;
1.000   0.000   16.130   3.150   1.400   1.000;
1.000   1.000   16.250   3.100   1.400   1.000;
1.000   0.000   16.040   3.250   3.200   1.000;
1.000   0.000   16.040   3.500   2.900   1.000;
1.000   0.000   16.070   1.400   1.000   1.000;
1.000   0.000   16.550   3.200   2.300   1.000;
1.000   0.000   16.120   2.800   2.000   0.500;
1.000   1.000   16.450   3.150   1.400   1.000;
1.000   0.000   15.910   3.400   1.600   1.000;
1.000   1.000   15.700   3.000   2.400   1.000;

Best,
Lucy Lurie (she/her/hers)
Doctoral Student, Clinical Psychology
Department of Psyc

Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

2021-06-09 Thread Iglesias Gonzalez, Juan E.

Dear Chester,
What command did you exactly run? There seems to be a mix of T1 and 
T1+additionalMRI segmentation commands in there.
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com 

> On Jun 9, 2021, at 00:23, Chester Kang  wrote:
> 
>External Email - Use Caution
> 
> Hello FreeSurfer Developers,
> 
> I am trying to run subfield segmentation of the hippocampus using Freesurfer 
> v7.1.0. Recon-all has been previously run on all subjects, however with a 
> different version of Freesurfer (v5.3.0). 
> 
> Getting the error(s): "No such file or directory" and on further 
> investigation "dyld: Library not loaded: @rpath/libmwlaunchermain.dylib"
> 
> I've searched the archive but could not find a solution.  
> 
> Could someone please help?
> 
> Below are details of the system and unsuccessful troubleshooting attempts.
> 
> Regards,
> Chester
> 
> 
> FreeSurfer version: 7.1.0
> Platform: Mac OS 10.13.3
> hippocampal-subfields-T1.log is below:
> 
> Things that have been checked/tried or troubleshooting attempted:
> - SIP protection is disabled (csrutil status shows "disabled")
> - Checked that there are files and correct permissions in the "lib/gcc/lib" 
> and the "MCRv84" folders
> - tried to unset DYLD_LIBRARY_PATH (in the SetUpFreeSurfer.sh)
> - checked the DYLD_LIBRARY_PATH value and run a step directly (both with "" 
> empty value and the values below)
> 
> $ echo $DYLD_LIBRARY_PATH
> 
> .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib
> 
> $ 
> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
> 
> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
>  
> dyld: Library not loaded: @rpath/libmwlaunchermain.dylib
>  Referenced from: 
> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1T2_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1T2_autoEstimateAlveusML
>  Reason: image not found
> Abort trap: 6
> 
> 
> 
> === hippocampal-subfields-T1.log ===
> 
> 
> "...
> --
> USER chester
> HOST selma.nnf.unimelb.edu.au
> PROCESSID 17656 
> PROCESSOR x86_64
> OS Darwin
> ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS 1 
> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 
> 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64
> --
> 
> freesurfer-darwin-macOS-7.1.0-20200511-813297b
> 
> setenv SUBJECTS_DIR /data/netapp02/work/chester/global_pass_all
> cd /data/netapp02/work/chester/global_pass_all
> /Applications/freesurfer_v7.1.0/bin/segmentHA_T1.sh 1002310
> 
> #
> #@# Hippocampal Subfields processing (T1) left Tue  8 Jun 2021 15:25:15 AEST
> --
> Setting up environment variables
> ---
> DYLD_LIBRARY_PATH is 
> .:/Applications/freesurfer_v7.1.0/MCRv84//runtime/maci64:/Applications/freesurfer_v7.1.0/MCRv84//bin/maci64:/Applications/freesurfer_v7.1.0/MCRv84//sys/os/maci64:/Applications/freesurfer_v7.1.0/lib/gcc/lib
> /Applications/freesurfer_v7.1.0/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
>  line 33: 
> /Applications/freesurfer_v7.1.0/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML:
>  No such file or directory
> Darwin selma.nnf.unimelb.edu.au 17.4.0 Darwin Kernel Version 17.4.0: Tue Dec 
> 19 10:52:05 PST 2017; root:xnu-4570.47.16~1/RELEASE_X86_64 x86_64
> 
> T1 hippocampal subfields exited with ERRORS at Tue  8 Jun 2021 15:25:16 AEST
> 
> ..."
> 
> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] recon-all errors

2021-06-09 Thread Mark Wagshul

External Email - Use Caution

Doug,

Following up on this. Where can I upload the data for you to take a look? 
Thanks,

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org

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This email message and any accompanying attachments may contain privileged 
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From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Tuesday, June 1, 2021 6:02 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all errors

OK, I'll have to take a look at the data. Someone will be in touch about 
getting it.

On 6/1/2021 11:02 AM, Mark Wagshul wrote:

External Email - Use Caution

External Email - Use Caution
It works fine in 6.0, was in 7.1. The registration looks fine (the FLAIR is 
brain extracted, while the orig.mgz is not, is this expected, or was that my 
error, I don't recall which FLAIR image I fed in).

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org

[einstein-logo-rgb]
This email message and any accompanying attachments may contain privileged 
information intended only for the named recipient(s). If you are not the 
intended recipient(s), you are hereby notified that the dissemination, 
distribution, and or copying of this message is strictly prohibited. If you 
receive this message in error, or are not the named recipient(s), please notify 
the sender at the email address above, delete this email from your computer, 
and destroy any copies in any form immediately.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 On Behalf Of Douglas N. Greve
Sent: Thursday, May 27, 2021 6:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all errors

Can you check the registration of the FLAIR and T1?
cd subject/mri
 tkregisterfv --mov orig/FLAIRraw.mgz --reg transforms/FLAIRraw.lta --targ 
orig.mgz



On 5/20/2021 4:33 PM, Mark Wagshul wrote:

External Email - Use Caution

External Email - Use Caution
Hi. I'm trying to run recon-all, with T1 and FLAIR images and running into 
errors, which seem to be associated with the FLAIR refinement of the pial 
surface.

recon-all -s 2019-10049-045-SP -FLAIR 
2019-10049-045-SP/VISIT_1/RAW/105_3D_FLAIR_SAGBrain.nii.gz -FLAIRpial -all


1.   Freesurfer version: 
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

2.   cat /proc/version:  Linux version 2.6.32-696.6.3.el6.694g.x86_64 
(root@-home-lgu-olaf-RHEL-6ES-9-x86_64.larkspur)
 (gcc version 4.4.7 20120313 (Red Hat 4.4.7-18) (GCC) ) #1 SMP Wed Jul 12 
02:19:57 UTC 2017

3.   uname -a: Linux loginnode2 2.6.32-696.6.3.el6.694g.x86_64 #1 SMP 
Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux

4.   recon-all.log attached

Thanks!

Mark


Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011
FAX: 718-430-3399
Email: mark.wags...@einsteinmed.org

[einstein-logo-rgb]
This email message and any accompanying attachments may contain privileged 
information intended only for the named recipient(s). If you are not the 
intended recipient(s), you are hereby notified that the dissemination, 
distribution, and or copying of this message is strictly prohibited. If you 
receive this message in error, or are not the named recipient(s), please notify 
the sender at the email address above, delete this email from your computer, 
and destroy any copies in any form immediately.






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Re: [Freesurfer] mri_hippocampal-subfields error: MATLAB exited for no reason (Iglesias Gonzalez, Juan E.) Re: Freesurfer Digest, Vol 208, Issue 17

[Freesurfer] Fw: Problem when using freesurfer

[Freesurfer] Samseg pallidum issue

[Freesurfer] mri_glmfit with pvr

[Freesurfer] LGI FS 7.1

[Freesurfer] Ill-Conditioned/Badly Scaled Matrix Error

Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

Re: [Freesurfer] recon-all errors

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