[Freesurfer] Qdec crash while analysis almost finished

[chenbh35]

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Hi, dear Freesurfer experts,




I recently came across an invalid Freesurfer license key error while using 
v5.3, and I tried apply for another license key, it just sent me the same 
license key as I have apply before. Then I put the licence file to 
/usr/local/freesurfer and has changed the name to .license as well. But it 
still doesn't work. Owing to the version I used last time was v6.0, so I 
reinstall a v6.0 and use the same license file. 

But here comes the new problem, when the analysis almost finished, qdec just 
crash and disappear, parts of the contents in the command window are:

""

Writing results
  lh-Avg-Intercept-thickness
maxvox sig=1e+10  F=3846.45  at  index 14 0 0seed=1611502349
  lh-Diff-PCE-CON-Intercept-thickness
maxvox sig=3.52355  F=15.3058  at  index 11472 0 0seed=1611502349
mri_glmfit done
ninputs = 2
Checking inputs
nframestot = 2
Allocing output
Done allocing
nframes = 2
Writing to /media/lava/DATA/ESSAY/FirstWave/qdec/Untitled/contrasts.sig.mgh

--
ERROR: Invalid FreeSurfer license key found in license file 
/usr/local/freesurfer/license.txt
  If you are outside the NMR-Martinos Center,
  go to 
http://secure-web.cisco.com/1l89yx4rr6CbgxQdMiHeY9D8oLAHswLvN7Y1eaaby-Qvn6BVAZuZXwQTAmP0xC7E_rBnRtenwucOyHla0XC9xw2XeIb4JxTVdGUe7DvwQWkZeHZrUqHnr9ytKduEorS6hP5vcMYSHddgx_sm5IuMyMwUIclL1iy7aEMQi4_WDwbqmWFSL9JHrJR0Pi8jESAhxmMm7PAdyF8HtflWq5QA7WU7ccAdPF1EbObmbe9JfgZ9HMqGuzIq5iaG5WpkQHMBFU-RRra2y1iv0boOXppQN-w/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu
 to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.


"""

I wonder what was the question?  Appreciate for any suggestions.___
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Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0

[Dowling, Kevin Francis]

cs Laboratory
Department of Psychiatry
Massachusetts General Hospital
MD/PhD Candidate
University of Pittsburgh &
Carnegie Mellon University MSTP



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Kevin F. Dowling
Per-Diem Clinical Research Coordinator
Brain Genomics Laboratory
Department of Psychiatry
Massachusetts General Hospital
MD/PhD Candidate
University of Pittsburgh &
Carnegie Mellon University MSTP
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[Freesurfer] matrix is ill-conditioned or badly scaled

[Julie Ottoy]

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Hi freesurfer experts,

I am trying to run a GLM fit between cortical thickness and some other
continuous marker. My cortical thickness were stacked before using the
mris_preproc and surf2surf commands.
I have an FSGD file with the same subjects as used during the stacking of
the thickness maps, but I added a new continuous regressor (my independent
variable of interest). However, some subjects have a missing value for this
regressor, so I added NaN. This makes me run into the following error. When
I replace the NaN values by random numbers in the FSGD, it all runs fine.

M = [ ...
 1.0  0.99577  0.70711  0.98278  0.97547 -0.97111  nan
 0.99577  1.0  0.70628  0.97775  0.97819 -0.95833  nan
 0.70711  0.70628  1.0  0.68252  0.70488 -0.70032  nan
 0.98278  0.97775  0.68252  1.0  0.95399 -0.96466  nan
 0.97547  0.97819  0.70488  0.95399  1.0 -0.92863  nan
-0.97111 -0.95833 -0.70032 -0.96466 -0.92863  1.0  nan
 nan  nan  nan  nan  nan  nan  nan  ]
Normalized matrix condition is 1e+08
Design matrix --

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.


I made sure that my FSGD file does not have any weird characters, so i
applied the cat fsgd.txt | sed 's/\r/\n/g' > new.fsgd.txt, but this also
didn't help.

Thank you for your help,
Julie
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Re: [Freesurfer] Ubuntu_710_clone-disk1 'developer' password

[fsbuild]

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Hello Adrian,
Sending the info to your email shortly.
- R.

On Jan 12, 2021, at 15:42, Adrian Ion - Margineanu 
adrian..ionmargine...@kuleuven.be 
wrote:External Email - Use 
CautionHi all,Can I please get 
the password for this image:Ubuntu_710_clone-disk1​ ?I am stuck at the 
'developer' login page 
..Cheers,Adrian___Freesurfer 
mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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[Freesurfer] Ubuntu_710_clone-disk1 'developer' password

[Adrian Ion - Margineanu]

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Hi all,


Can I please get the password for this image: Ubuntu_710_clone-disk1? ?


I am stuck at the 'developer' login page ..


Cheers,

Adrian
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[Freesurfer] Postdoc and RA positions @ UConn/UCSF brainLENS Lab

[Jieyin Feng]

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Hi all,

Fumiko Hoeft MD PhD, Professor of the Departments of Psychological
Sciences, Mathematics, Neuroscience and Psychiatry (
https://secure-web.cisco.com/1jarcQIUIbQjv36uDq2UMAWtM3a1o32H28Un4BykAlrsFg6BvNr1OaA5-3ehyC7k3wY9TF-6CCf6NRBe11QHs3o1e1Ec2cWtc7eBUi5AmiTmZPMMfGBA0SsWA2OPoln6U9mR9XaPWakE0ZxqHNZpK_OmicCbitD7Y6aOceA0Y74hQ6-MA3MkMg4p4kOBX1g6gVbrl1GsOBr4Z2wX2jtNQhx3HqNhQ7__3Pqo0VrZwuP9h_xBjSDhPqPn6PwGRwtnGter1QzFdiJ42wP2PfTSwAQ/https%3A%2F%2Fpsych.uconn.edu%2Fperson%2Ffumiko-hoeft%2F),
 and Director of the Brain
Imaging Research Center 
(https://secure-web.cisco.com/1W4BQ4p5O8b2VkVODa9Ukl2K0jZWyfT1Gpv42RvMWqO9LDBsZTq9nqDcnNp8XTduhxGSEyUvhVzd0UtokbYlMxzNgkEofGEkmcv1GNefjS-S1GQN9cfuNieyhsdz3sq6PsbO1XU5XC5XnoUcywEBoJ9XKzPU7ytFqAGQnMuiiVQUsAwSGp2g1CDUJA8sqo7OmPo-7dXaSulz0FZWU52gzmhKjpvATMym9qZ3kWznRbcoq9ffP_t3TUU-APvJGK02U_Lg1jwV-9kTofF-RTAZbyA/https%3A%2F%2Fbirc.uconn.edu)
 at UConn, and Adjunct
Professor of Psychiatry and Behavioral Sciences at UCSF, is now accepting
additional applications of up to two postdoctoral fellows and/or research
assistants (RAs) to *begin sometime between now and the fall of 2021 at
UConn (possibly at UCSF for postdocs*; 
https://secure-web.cisco.com/1wvOkW2Jb_7WnClFkK869jkPXXQlvYMUYHZBpASrvjJIndwQWo926cgDKWEWp0CyLmHS4ZJIekgoRwSlH7y8RvYW5VALjeBcw3exOKAqbYvVU6jB3XTs58Fshm2paSRlYtWznxMFXix9jxOZDv2ev9_DVAvwKtVBAtBZYwOaOqneowUr5zaMZcWZeCZB0b5146mhF2i7iUbjzcbRX7cDLCsQaIwH8sBm8YIc8XP6Fij_SSADcpfkX44zHBpahbShMy1j17AB4WamT9VXg3OZDUA/https%3A%2F%2Fwww.brainlens.org).
The *postdoc(s)* would ideally have strong research- and
publication-records in: (1) reading, dyslexia or related fields of
(developmental) cognitive neuroscience; or (2) fetal, neonatal or infant
neuroimaging. The latter does not have to be in reading/dyslexia, and can
be in affective neuroscience. Experience in interdisciplinary research is a
plus; from theory, multimodal neuroimaging (fMRI, dMRI, TMS, MRS, EEG,
etc), genetics, machine learning and network approaches (see
https://secure-web.cisco.com/1hBEx0yvAY8RBzyK3W1LPLkb-Wz1W0Co4pLBYErp76Cbfiir7h1gvIs7wRJf_AxrekXnVKHJJrmhWSWaCvRDmzWbP5meMKNQ4CP0M4oHy_LRfqJKumj9OjKIsmqHB-dOvzmQFRm1VOGA-pgk2sOxmRPL0UpTiR45oKtJRTgKe1MEbcUfI5ryNWsHaDlz7oJG9umI9PRQSlhGJR_TgBCBliTNkFh1RHaq3-XrsqcDRGH-BrQ2NxlPhhaJRF3ARo2VOiLMneJnVOalfyafueSsovg/https%3A%2F%2Fwww.brainlens.org%2Femployment).
 The *RAs* would ideally have
experience in the areas above, though not required. Strong management,
organizational and communication/writing skills are required. Programming
skills are desired but not required. There are opportunities to write
grants, and publish using many of our existing and publicly available
datasets. The positions are fully funded, primarily by NIH grants though a
US citizenship is not required.
Interested applicants should submit a cover letter, full CV, names of 3
references, and preferred location (UConn or UCSF) to Prof. Fumiko Hoeft at
brainl...@uconn.edu. When you write, please use subject, “[Postdoc] FIRST &
LAST NAME” of “[RA] FIRST & LAST NAME”.
Thanks,
Jieyin
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Re: [Freesurfer] Anterior insula thickness {Disarmed}

[Vera, Matthew]

Hello Hanne,

I’ll take a look with you and hopefully we can figure this out. Just to 
clarify, the mris_divide_parcellation outputs lh.aparc.splittedinsula.annot, 
but this is saved as a text file like lh.aparc.splittedinsula.txt?

Thanks so much!
Matt

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

Date: Wednesday, December 30, 2020 at 10:29 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Anterior insula thickness {Disarmed}

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Dear experts,

I am trying to divide the insula into two parts, in order to calculate the 
thickness of only the anterior region. I used the command 
mris_divide_parcellation on the aparc.annot file (see below), with a text file 
that indicated which region needs to be split (splittable.txt). The issue is 
that it does generate a file, but as a document and not an annotation file. 
Supposedly the issue is with the seed (see last output line error). When trying 
to use this file regardless, to make the labels, it does not generate any 
labels (see second command and output).

Do you perhaps have a suggestion how I could fix this?

Best,

Hanne

Parcellation command:
mris_divide_parcellation fsaverage lh lh.aparc.annot splittable.txt 
lh.aparc.splittedinsula.annot

Output:
reading colortable from annotation file...
colortable with 1036 entries read (originally 
/scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)
interpreting 4th command line arg as split file name
dividing insula (1035) into 2 parts
allocating new colortable with 36 additional units...
 supposed to be reproducible but seed not set
saving annotation to lh.aparc.splittedinsula.annot


Annot to label command:
mri_annotation2label --subject fsaverage --hemi lh --annotation 
lh.aparc.splittedinsula.annot --outdir ..

Output:
subject = fsaverage
annotation = 
/Applications/freesurfer/FS/fsaverage/label/lh.aparc.splittedinsula.annot
hemi = lh
outdir = ..
surface   = white

Reading surface
 /Applications/freesurfer/subjects/fsaverage/surf/lh.white
Loading annotations from 
/Applications/freesurfer/FS/fsaverage/label/lh.aparc.splittedinsula.annot
reading colortable from annotation file...
colortable with 1072 entries read (originally none)
Seg base 0
max index = 1037
Segmentation fault: 11


On 23 Dec 2020, at 19:02, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:

We don't have an anterior insula segmentation. One thin you can try is to 
divide the insula label with mris_divide_parcellation. If one of those 
subdivisions works for you then you can compute the thickness inside it. You 
might want to do it on fsaverage and then map it back to the individual 
subjects. Or you can just draw the label you want on fsaverage and map it back 
to the individual subjects
On 12/21/2020 9:34 AM, Hanne Van Der Heijden wrote:
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Dear freesurfer experts,

I have a question regarding analysis of cortical thickness.
In the stats folder of each subject, the {hemi}.aparc.stats file gives the 
thickness of several areas, one of them being the insula. Is it possible to get 
only the anterior insula thickness?

Thank you in advance, and I hope to hear from you soon.

Best,

Hanne van der Heijden



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Re: [Freesurfer] eTIV=0.0 on volumes where control points have been added manually

[Greve, Douglas N.,Ph.D.]

Hi Julia, this is a bug. We've fixed it in our development version, but for you 
there are a few option. One is that you can just get the value from aseg.stats 
(asegstats2table). Or you can run recon-all with these flags -talairach 
-parcstats -parcstats2 -parcstats3

On 12/29/2020 7:34 AM, Julia Lam wrote:

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Dear all,

I received values of 0.0 on variables BrainSegVolNotVent and eTIV when running 
aparcstats2table on volumes where I've added control points. However, when 
aseg2stats was used, the variable EstimatedTotalIntraCranialVol was different 
from 0 on all, including the edited ones. Why is that?

I've attached the logfile from one of the subjects where I used control points.

I really appreciate any help you can provide.

Yours sincerely
Julia Lam






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Re: [Freesurfer] Freesurfer Digest, Vol 202, Issue 36 Topic 14. Error with command: mri_em_register: RB40_talairach_2005-07-20.gca. No such file or directory (Greve, Douglas N., Ph.D.)

[Greve, Douglas N.,Ph.D.]

Sorry, I lost track of the original thread. Can you explain it or say why you 
are not running recon-all?

On 1/4/2021 9:27 AM, Camerino, I.L. (Ileana) wrote:

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Dear Douglas,

Thank you so much for your reply.

After trying: mri_em_register -mask brain.mgz -p .5 nu.mgz 
$FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta
I got the following error:  using MR volume brain.mgz to mask input volume...
using top 50.0% wm points as control points

== Number of threads available to mri_em_register for OpenMP = 1 ==
reading 1 input volumes...
logging results to talairach.log
reading '/opt/freesurfer/6.0/average/RB_all_2016-05-10.vc700.gca'...
average std = 7.3   using min determinant for regularization = 5.3
0 singular and 841 ill-conditioned covariance matrices regularized
reading 'nu.mgz'...
mghRead(/project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/mri/brain.mgz, 
-1): could not open file
mri_em_register: could not open mask volume brain.mgz.

In fact the the file brain.mgz is not present in the mri folder.

I am a bit lost since I am getting a different error every time I try to solve 
the previous one and I do not understand what is the problem exactly.

The first error I got after running recon all on this subject (with a massive 
stroke on the left hemisphere) is a watershed error. So I added the control 
points and run:  recon-all -autorecon2-cp -autorecon3 -subjid 
/project/3015068.01/ilecam/Reolang/Freesurfer/sub-056. After which I got the 
error:

mghRead(/project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/mri/norm.mgz, 
-1): could not open file
assuming input volume is MGH (Van der Kouwe) MP-RAGE
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
mri_normalize: could not open source file norm.mgz

Finally to solve the above error I run: mri_em_register -mask brain.mgz -p .5 
nu.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca 
transforms/talairach.lta but I got yet a new error: -1): could not open file 
mri_em_register: could not open mask volume brain.mgz.

Please could you let me know how can I understand what is the problem and how 
can I solve it?

Best regards
Ileana Camerino

PhD candidate
Donders Institute for Brain, Cognition and Behaviour

Centre for Cognition
Spinozabuilding
Room B02.25
Montessorilaan 3, 6525 HR Nijmegen
The Netherlands
Tel. +31-24 3612618







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Re: [Freesurfer] Transform rescaled non-pvc PET to surface

[Julie Ottoy]

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Hi Doug,

Thank you!
Is that the same output as using mri_gtmpvc with --psf 0 --no-tfe and look
at the mgx.ctxgm.nii.gz ?

Thanks
Julie

On Tue, 12 Jan 2021 at 10:39, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> If you've run mri_gtmpvc already, you can add --save-input and it will
> save a file called input.rescaled.nii.gz which will be rescaled to your
> reference region
>
> On 12/29/2020 4:19 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Dear Freesurfer team,
>
> I have a question related to petsurfer. On the website, it is stated that "If
> you are not using PVC, you can use the template.reg.lta to sample the PET
> volume onto the surface using mri_vol2surf, then apply standard
> surface-based analysis."
>
> However, I was wondering how to do this for PET data that I first want to
> normalize to a reference region (to perform group-wise glm analyses
> afterwards). For example, I want to transform the "non-pvc and
> pons-rescaled PET volume" to the surface. Is there a way to easily do this?
> Or should I use the --scale flag with vol2surf and input the non-pvc
> reference region value for each subject reading from the gtm.stats.dat
> file, which I got from the mri_gtmpvc with --psf 0 --no-tfe --no-rescale?
>
> Thank you for the help!
> Best regards
> Julie
>
>
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Re: [Freesurfer] recon-all -hires option

[Greve, Douglas N.,Ph.D.]

If you want to try to do it systematically, you can add -wsless (should reduce 
the agressiveness of the skull strip)

On 1/4/2021 3:52 AM, 
falk.luesebr...@med.ovgu.de wrote:

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Hi Simon,


in case your surfaces (and other outputs) look fine, there is no need to worry 
about the skull stripping too much. However, in case you what to do something 
about this you can do either of the following.


Which version are you using? I assume v6? In v7 the hires option basically has 
changed to what was known as the HCP pipeline before. Here, only the surface 
related parts of FreeSurfer are handled in native space. The other stages are 
handled in resampled 1mm space. Therefore, you will benefit from your higher 
resolution, while not having any of these issues. There are also some other 
stages included which may help with high resolution 3T data (e.g. denoising 
prior to surface placement).


In case you want to stick with v6 and what to run everything in native space, 
you can get better skull stripping following the first few steps from this 
guide I put together few years ago (and is still valid today):

https://secure-web.cisco.com/1cP9GZTFwQIDCR-WcWJPQA-tzd6FKvDGnFtvVRx4GcsgT8p3OTg1qClc-Hq--pwQhCCzMU0__8jGrDJugvajjUrRsHuOiOAOaxFIABpq99gkP60a9dQB2KDoTXXK3jmPU66oLOS0VCPGhxL5_1DVsdUVWefugGXKw6nA29BxCzBaKOfrZBOuL4bxxOBVIVUa1E3EfYzL7gMPd6g5Xvqz1zUtRdv-sQtDWX98QT7ZaoRAjjeDZvgWcqjhe9WNHXE5kInE_ok7pb2gunRxE78zPKg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHiResRecon


What you basically do is to run the 1mm stream to create a nice brainmask (or 
any other tool you like), resample that to the resolution of your high 
resolution stream and apply the mask after the normalization stage. Then 
continue with autorecon2 and autrecon3.


Best,

Falk



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

 im Auftrag von S.R. Poortman 

Gesendet: Montag, 4. Januar 2021 09:13:11
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] Fw: recon-all -hires option


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Dear list members,

As a PhD student working on longitudinal child and adolescent T1-weighted data 
(.75x.75x.8 mm3) acquired at 3T (age range: 8 - 18 at baseline; 11 - 24 at 
follow-up), with the aim of doing cortical laminar analyses eventually, I am 
interested in getting the most of our lab's submillimeter resolution data. 
Therefore, in addition to a default recon-all run (with the -3T option 
enabled), I ran a separate recon-all with both the -3T and the -hires option 
enabled (with mris_inflate -n 50 added to the expert file), resulting in the 
following two runs:
recon-all -all -i ${subj} -subjid ${SUB_ID} -3T
and
recon-all -all -i ${subj} -subjid ${SUB_ID}  -3T -hires -expert $EXPERT_FILE
Now, the surfaces (i.e., lh.pial, lh.white, rh.pial, rh.white) seem to be 
calculated more accurately for most brain regions, indeed, which looks very 
promising. However, the brainmask.mgz turns out to be of poor quality for a 
number of our subjects, cutting away a substantial portion of the brain. See 
the image below for an example of the same subject, on which both runs have 
been performed. The same slices are shown for each run. As can be seen in the 
image, a part of the the temporal region of the brain has been excluded in the 
brainmask.mgz of the -hires run (left in the image).

[cid:b4d26f40-11bb-4d8f-888c-ab4da9fea062]

Is there anything I can do, such as adjusting certain parameters, to prevent 
this from occurring? It would be a shame if I couldn't make use of the -hires 
option due to this, as it does seem to be a promising option in all other 
aspects.

Thank you for considering my question. I look forward to hearing from you.

Good holidays to you!

Kind regards,
Simon Poortman (Erasmus MC, Rotterdam, the Netherlands)





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Re: [Freesurfer] Segmentation Fault During mri_convert running FS 5.0

[Greve, Douglas N.,Ph.D.]

For some reason, it is not capturing the terminal output in the log files. Can 
you just run
mri_convert 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
 deleteme.mgz
and send me the terminal output?

On 1/2/2021 2:23 PM, Dowling, Kevin Francis wrote:
Hello FreeSurfer experts,

We have some old clinical structural data we processed using version 5.0 and 
had extensively edited manually. We’re now hoping to re-process the data in 
version 5 to regenerate copies of the subjects that are free of manual edits. 
So far (because of the below core dump error), I’ve tried doing this two ways, 
first by running recon-all -autorecon-all -clean -s  on copies of our 
manually edited data and, secondly, by using from the original, unaltered 
MPRAGE files and running recon-all -i ./path/to/MEMPRAGE.nii -s  
(which fails before we would then run recon-all -autorecon-all -s ). 
In both cases I’ve run into an error I never encountered when last working with 
this data 2 years ago in version 5. Specifically I get a “Segmentation fault 
(core dumped)” when mri_convert is invoked. I’ve enclosed a copy of the 
recon-all.log and recon-all.error files as attachments and provided the 
specific commands that seem to trigger the core dump below (from 
recon-all.error file). I looked on the mail archive but I wasn’t able to find 
any answers.

I’m running version 5.0 (as that is the version our manually edited data was 
processed in):
setenv USE_STABLE_5_0_0
source /usr/local/freesurfer/nmr-stable50-env

build stamp: freesurfer-Linux-centos4_x86_64-stable-v5.0.0-20110319
I’m running Red Hat Enterprise Linux Release 6.7 (Santiago)

The specific commands that appear to be causing the (Segmentation fault) core 
dump in each of the two different cases are below (taken from recon error log):

When running: recon-all -i ./path/to/MEMPRAGE.nii -s  the error occurs 
with..
mri_convert 
/autofs/cluster/deplin/chris/data/Selected_Scans/3800033/MPRAGE/003/MEMPRAGE.nii
 /autofs/cluster/roffman2/users/RPDR_FromRaw_No_Edits/00033/mri/orig/001.mgz

When running: recon-all -autorecon-all -clean -s  the error occurs 
with..
mri_convert 
/autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/rawavg.mgz 
/autofs/cluster/roffman2/users/RPDR_No_Manual_Edits/00033_E/mri/orig.mgz 
--conform

Notably, when I tried running the same commands (bolded above) in version 5.3 
(source/usr/local/freesurfer/nmr-stable53-env) they both exit without errors, 
leading me to wonder if this is a software-version interaction issue. (In case 
it has any bearing, I’m running all of this while ssh’d into the Martinos 
servers.)

I suspect I may have missed something very simple, but I would be very grateful 
for any suggestions for how I might try to overcome this issue. I’m happy to 
provide clarification or any additional information that may be helpful.

Thank you,
Kevin

Kevin F. Dowling
Per-Diem Clinical Research Coordinator
Brain Genomics Laboratory
Department of Psychiatry
Massachusetts General Hospital
MD/PhD Candidate
University of Pittsburgh &
Carnegie Mellon University MSTP



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Re: [Freesurfer] The lookuptable value of Virchow–Robin space

[Greve, Douglas N.,Ph.D.]

Probably
77  WM-hypointensities  200 70  255 0


On 1/2/2021 1:11 PM, Aaron Tanenbaum wrote:

External Email - Use Caution

Ideally, what should Virchow–Robin space be labeled as.



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Re: [Freesurfer] Transform rescaled non-pvc PET to surface

[Greve, Douglas N.,Ph.D.]

If you've run mri_gtmpvc already, you can add --save-input and it will save a 
file called input.rescaled.nii.gz which will be rescaled to your reference 
region

On 12/29/2020 4:19 PM, Julie Ottoy wrote:

External Email - Use Caution

Dear Freesurfer team,

I have a question related to petsurfer. On the website, it is stated that "If 
you are not using PVC, you can use the template.reg.lta to sample the PET 
volume onto the surface using mri_vol2surf, then apply standard surface-based 
analysis."

However, I was wondering how to do this for PET data that I first want to 
normalize to a reference region (to perform group-wise glm analyses 
afterwards). For example, I want to transform the "non-pvc and pons-rescaled 
PET volume" to the surface. Is there a way to easily do this? Or should I use 
the --scale flag with vol2surf and input the non-pvc reference region value for 
each subject reading from the gtm.stats.dat file, which I got from the 
mri_gtmpvc with --psf 0 --no-tfe --no-rescale?

Thank you for the help!
Best regards
Julie




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Re: [Freesurfer] Failed tissue type check {Disarmed}

[Julie Ottoy]

External Email - Use Caution

Hi Doug

I tried that as well but getting the same error as with --replace 29 3.

ERROR: CTABpruneCTab(): ctab does not have segid 2


Thanks,
julie

On Tue, 12 Jan 2021 at 10:35, Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Try using --replace 29 2
>
>
> On 12/29/2020 12:48 PM, Julie Ottoy wrote:
>
> External Email - Use Caution
> Hi Doug
>
> Thanks for your reply. I tried both your suggestions, but it seems as
> though they both ran into an error.
>
> For your first suggestion, i.e. adding --replace 29 3 to the command line
> of gtmpvc, I get the error:
>
> Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz
>
> Loading seg ctab 057_S_5295re/mri/gtmseg.ctab
>
> Reading 057_S_5295re/mri/gtmseg.lta
>
> Replacing 19
>
> Pruning ctab
>
> ERROR: CTABpruneCTab(): ctab does not have segid 3
>
>
> For your second suggestion, i.e. I replaced the following line in the ctab:
>
>   29  Left-undetermined   135 206 2350  -1
>
> ==> replaced by:  29  Left-undetermined   135 206 2350  3
>
>
> I get the error:
>
> Computing Seg in input space
>
> Building GTM DoVoxFracCor=0
>
> ERROR: creating region for nthseg=12, segid=29, Left-undetermined
>
> It may be that there are no voxels for this seg when mapped into the input
> space.
>
> Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the
> registration
>
>  Build time 5.9690, err = 1
>
>
> Thank you,
>
> Julie
>
> On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> You can use the fix from my previous email or you can add the following
>> line any were into the gtmseg.ctab file:
>>  29  Left-undetermined   135 206 235 0 3
>>
>>
>> On 12/18/2020 11:06 PM, Julie Ottoy wrote:
>>
>> External Email - Use Caution
>> Sorry I would like to correct my previous post. The subject also failed
>> with PVC.
>> I see now that the issue is happening during the gtm seg stage where it
>> gives the error: WARNING: segid   29 Left-undetermined tissue type is not
>> set.
>> For your information: I ran the standard FS and petsurfer pipeline as
>> outlined on the wiki. I tried two gtm seg commands:
>> gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
>> gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm
>> --subseg-cblum-wm
>>
>> Thank you for your help,
>> Julie
>>
>> On Fri, 18 Dec 2020 at 00:09, Julie Ottoy 
>> wrote:
>>
>>> External Email - Use Caution
>>> Dear Doug,
>>>
>>> I have the same issue as the people below. I was wondering if this was
>>> solved in the meantime.
>>>
>>> I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and
>>> got the following error in only one of my subjects. When I ran the same
>>> subject with PVC and specified psf, it did run fine.
>>>
>>> $Id: mri_gtmpvc.c,-
>>> setenv -
>>> cd -
>>> mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg
>>> gtmseg.mgz --default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o
>>> /gtmnopvc.output.ceregrey --rescale 8 47
>>> sysname  Linux
>>> hostname -
>>> machine  -
>>> user -
>>> vgthresh   0.001000
>>> nReplace   18
>>> 0. 0. 0. 0. 0. 0.
>>> 24 avail.processors, using 1
>>> Creating output directory /gtmnopvc.output.ceregrey
>>> Loading seg for gtm /ID/mri/gtmseg.mgz
>>> Loading seg ctab /ID/mri/gtmseg.ctab
>>> Reading /ID/mri/gtmseg.lta
>>> Replacing 18
>>> Pruning ctab
>>> Checking tissue type
>>> ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not
>>> set
>>> Failed tissue type check
>>>
>>> Any suggestions would be appreciated!
>>> Thank you,
>>> Julie
>>>
>>> Re: [Freesurfer] mri_gtmpvc error: failed tissue type check
>>> 
>>> 2017-11-25
>>> 
>>>  Thread
>>> 

Re: [Freesurfer] Failed tissue type check {Disarmed}

[Greve, Douglas N.,Ph.D.]

Try using --replace 29 2


On 12/29/2020 12:48 PM, Julie Ottoy wrote:

External Email - Use Caution

Hi Doug

Thanks for your reply. I tried both your suggestions, but it seems as though 
they both ran into an error.

For your first suggestion, i.e. adding --replace 29 3 to the command line of 
gtmpvc, I get the error:

Loading seg for gtm 057_S_5295re/mri/gtmseg.mgz

Loading seg ctab 057_S_5295re/mri/gtmseg.ctab

Reading 057_S_5295re/mri/gtmseg.lta

Replacing 19

Pruning ctab

ERROR: CTABpruneCTab(): ctab does not have segid 3


For your second suggestion, i.e. I replaced the following line in the ctab:

  29  Left-undetermined   135 206 2350  -1

==> replaced by:  29  Left-undetermined   135 206 2350  3


I get the error:

Computing Seg in input space

Building GTM DoVoxFracCor=0

ERROR: creating region for nthseg=12, segid=29, Left-undetermined

It may be that there are no voxels for this seg when mapped into the input 
space.

Check 057_S_5295/057_S_5295.gtmnopvc.output.pons/aux/seg.nii.gz and the 
registration

 Build time 5.9690, err = 1


Thank you,

Julie

On Wed, 23 Dec 2020 at 12:48, Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>> wrote:
You can use the fix from my previous email or you can add the following line 
any were into the gtmseg.ctab file:
 29  Left-undetermined   135 206 235 0 3


On 12/18/2020 11:06 PM, Julie Ottoy wrote:

External Email - Use Caution

Sorry I would like to correct my previous post. The subject also failed with 
PVC.
I see now that the issue is happening during the gtm seg stage where it gives 
the error: WARNING: segid   29 Left-undetermined tissue type is not set.
For your information: I ran the standard FS and petsurfer pipeline as outlined 
on the wiki. I tried two gtm seg commands:
gtmseg --s ${id} --xcerseg --keep-hypo --subsegwm --subseg-cblum-wm
gtmseg --s ${id} --keep-cc --no-xcerseg --keep-hypo --subsegwm --subseg-cblum-wm

Thank you for your help,
Julie

On Fri, 18 Dec 2020 at 00:09, Julie Ottoy 
mailto:julie.jj.ot...@gmail.com>> wrote:

External Email - Use Caution

Dear Doug,

I have the same issue as the people below. I was wondering if this was solved 
in the meantime.

I ran petsurfer gtmpvc with the psf 0 and no-tfe flags to not do PVC and got 
the following error in only one of my subjects. When I ran the same subject 
with PVC and specified psf, it did run fine.

$Id: mri_gtmpvc.c,-
setenv -
cd -
mri_gtmpvc --i /input.nii.gz --reg PET.lta --psf 0 --no-tfe --seg gtmseg.mgz 
--default-seg-merge --auto-mask 10 0.01 --mgx 0.01 --o 
/gtmnopvc.output.ceregrey --rescale 8 47
sysname  Linux
hostname -
machine  -
user -
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
24 avail.processors, using 1
Creating output directory /gtmnopvc.output.ceregrey
Loading seg for gtm /ID/mri/gtmseg.mgz
Loading seg ctab /ID/mri/gtmseg.ctab
Reading /ID/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set
Failed tissue type check

Any suggestions would be appreciated!
Thank you,
Julie

Re: [Freesurfer] mri_gtmpvc error: failed tissue type 
check
2017-11-25
 
Thread
 Douglas 

[Freesurfer] eTIV=0.0 on volumes where control points have been added manually

[Julia Lam]

External Email - Use Caution

Dear all,

I received values of 0.0 on variables BrainSegVolNotVent and eTIV when running 
aparcstats2table on volumes where I've added control points. Why is that? 

I really appreciate any help you can provide.

Yours sincerely
Julia Lam

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