Re: [Freesurfer] Amygdala Segmentation T1.v20 Command

[Iglesias Gonzalez, Juan E.]

Thanks, Wisteria. Can you please send us the list of files under the mri 
directory of any subject?
Cheers,
/Eugenio

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


From:  on behalf of "Deng, Yushan 
Wisteria" 
Reply-To: Freesurfer support list 
Date: Tuesday, 7 January 2020 at 21:04
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: Re: [Freesurfer] Amygdala Segmentation T1.v20 Command

Hi Eugenio,

Thank you so much for your response! I did use the development version to run 
the command. Would you have any other ideas what the possible cause might be?

Best,
Wisteria

Date: Tue, 7 Jan 2020 09:05:32 +
From: "Iglesias Gonzalez, Juan E." 
mailto:jiglesiasgonza...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Amygdala Segmentation T1.v20 Command
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: 
<8970525b-ed9a-4f56-901a-50f5787c9...@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Dear Wisteria,
Did you run the command segmentHA_T1.sh on those subjects using the development 
version?
Cheers,
/Eugenio

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


From: 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of "Deng, Yushan Wisteria" 
mailto:ywd...@mgh.harvard.edu>>
Reply-To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Friday, 3 January 2020 at 20:31
To: "freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Amygdala Segmentation T1.v20 Command

Dear Freesurfer experts,

Happy new year!

I encountered an issue with the quantifyHAsubregions.sh command as I tried to 
extract amygdala subnuclei values from a previously segmented dataset. I tried 
both commands below, specifying the version (v20) and not:
quantifyHAsubregions.sh amygNuc T1 All_Amyg [subjects_dir]
quantifyHAsubregions.sh amygNuc T1.v20 All_Amyg [subjects_dir]

The command did not run. No error message was given. It just skipped to a new 
command line. Please see attached for a screenshot.

The recon was done in Freesurfer 5.3 and the sample size is very big (~1400). I 
wonder if that or anything else could be causing the problem. Any guidance is 
immensely appreciated!

Thank you!
Wisteria


Wisteria Deng
Clinical Research Coordinator
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, Rm 2611
Charlestown, MA 02129
Phone: 617-643-4441


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[Freesurfer] RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca public permissions

[Kostakis Gkiatis]

External Email - Use Caution

Dear Freesurfer experts,
I am trying to compile freesurfer from source. It is nicely performed 
expect the "git annex get ." command which fails in these two files, 
RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca.
I searched github's annex branch but no sign of the files. Do I have, as 
public, the right permissions to download them? Can I find these two 
files somewhere else?

Thank you in advance.
Yours sincerely,
Kostakis
-- 
Electrical and Computer Engineer
Phd Candidate in Brain Imaging
Medical Image Processing, Algorithms and Applications
National Technical University of Athens
9,Iroon Polytechneiou str.,
157 73 Zografou Campus,
Athens, GREECE
phone:+30 210 772 3577

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[Freesurfer] Projection on fsaverage5

[Marina Fernández]

External Email - Use Caution

Dear Freesurfer experts,

I would like to convert the individual preprocessed EPI volume (that it is
normalized to MNI152 space and without smoothing) to surface and project it
on fsaverage5.  I used the following command:
mri_vol2surf --mov EPI.nii --reg register.dat --hemi [l/r]h --projfrac 0.5
--interp trilinear --trgsubject ico --icoorder 5 --o EPI_surface.mgh

Is it correct? Then, I tried to project the surface in fsaverage5 and it
seems to be rotated (it doesn't match).
What should I do to project it correctly?

Thank you in advance.
Best regards,
Marina.
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Re: [Freesurfer] Projection on fsaverage5

[Bruce Fischl]

Hi Marina

how do you project to fsaverage5?
cheers
Bruce
On Wed, 8 Jan 2020, Marina Fernández wrote:



External Email - Use Caution

Dear Freesurfer experts,
I would like to convert the individual preprocessed EPI volume (that it is
normalized to MNI152 space and without smoothing) to surface and project it
on fsaverage5.  I used the following command:
mri_vol2surf --mov EPI.nii --reg register.dat --hemi [l/r]h --projfrac 0.5
--interp trilinear --trgsubject ico --icoorder 5 --o EPI_surface.mgh

Is it correct? Then, I tried to project the surface in fsaverage5 and it
seems to be rotated (it doesn't match).
What should I do to project it correctly?

Thank you in advance.
Best regards,
Marina.

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Re: [Freesurfer] Projection on fsaverage5

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

Use --trgsubject fsaverage5 (you might have to link it to your 
SUBJECTS_DIR). Also, how did you compute the register.dat? If you've 
normalized it to MNI152, that will complicate things. Was the 
normalization linear and nonlinear?

On 1/8/20 8:03 AM, Marina Fernández wrote:
>
> External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I would like to convert the individual preprocessed EPI volume (that 
> it is normalized to MNI152 space and without smoothing) to surface and 
> project it on fsaverage5.  I used the following command:
> mri_vol2surf --mov EPI.nii --reg register.dat --hemi [l/r]h --projfrac 
> 0.5 --interp trilinear --trgsubject ico --icoorder 5 --o EPI_surface.mgh
>
> Is it correct? Then, I tried to project the surface in fsaverage5 and 
> it seems to be rotated (it doesn't match).
> What should I do to project it correctly?
>
> Thank you in advance.
> Best regards,
> Marina.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] FsFast Question

[Swetara Joshi]

External Email - Use Caution

Hello,

I am new to fmri processing/FsFast and I had a question on creating nuisance 
variables. Is it possible to set a block-design task fMRI paradigm file as a 
nuisance variable, so that it can be inputted at a .dat file for the  
mkanalysis-sess command?

Thank you!

Best,
Sweta



Sweta Joshi

Research Assistant

Department of Neurology

-

GW Medical Faculty Associates

George Washington University Hospital

2150 Pennsylvania Ave, NW, 9th Floor, Washington, DC 20037

Office: 202.655.5888

Email: sjo...@mfa.gwu.edu



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Re: [Freesurfer] (no subject)

[Boris Rauchmann]

External Email - Use Caution

Ok. i figured it out. The problem was just that you can not specify the
file type - so .mgz in  BN_Atlas_subcotex.mgz was actually the problem.

Now I run in a new issue:

gtmseg --head BN_apas+head.mgz --s 1122_test --o NEU_BN.gtmseg.mgz
--ctx-annot BN_Atlas.annot --ctab
'/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt'

Wed Jan  8 17:04:12 CET 2020

setenv SUBJECTS_DIR
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
cd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
/usr/local/freesurfer/bin/gtmseg --head BN_apas+head.mgz --s 1122_test --o
NEU_BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt

freesurfer-linux-centos6_x86_64-dev-20180911-69aa645
$Id: gtmseg,v 1.19 2016/03/24 17:32:23 greve Exp $
Linux linuxrechner2 4.15.0-65-generic #74~16.04.1-Ubuntu SMP Wed Sep 18
09:51:44 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas
BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
--no-subseg-wm --no-keep-cc --no-keep-hypo

$Id: mri_gtmseg.c,v 1.10 2016/08/02 21:07:24 greve Exp $
cwd /media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects
cmdline mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas
BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
--no-subseg-wm --no-keep-cc --no-keep-hypo
sysname  Linux
hostname linuxrechner2
machine  x86_64
user demenzbild
subject 1122_test
USF 2
OutputUSF 2
apasfile BN_apas+head.mgz
wmannotfile NULL
ctxannotfile BN_Atlas.annot
ctxlhbase 1000
ctxrhbase 2000
SubSegWM   0
KeepHypo   0
KeepCC   0
dmax 5.00
nlist   0
lhmin  1000
lhmax  1900
rhmin  2000
rhmax  2900
mri_gtmseg supposed to be reproducible but seed not set
Starting MRIgtmSeg()
Starting MRIgtmSeg() USF=2
Loading
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/1122_test/mri/BN_apas+head.mgz
Loading surfaces  t = 2.1510
Loading annotations  t = 4.8510
Not segmenting WM
reading colortable from annotation file...
colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt)
reading colortable from annotation file...
colortable with 211 entries read (originally ./BN_Atlas_210_LUT.txt)
 Relabeling any unlateralized hypointenities as lateralized hypointenities
  MRIrelabelHypoHemi(): looping over volume
 nthreads = 1
 Relabeling CC as WM
 Relabeling any hypointensities as WM
  MRIunsegmentWM(): looping over volume
 nthreads = 1
Upsampling segmentation USF = 2 t = 7.3520
  MRIhiresSeg(): filling unknowns with 257
Beginning cortical segmentation using BN_Atlas.annot t = 41.3800
  MRIannot2CorticalSeg(): looping over volume
 nthreads = 1
  MRIannot2CorticalSeg(): found 2347 unknown, filled with 257
Not subsegmenting WM
Found 279 segs in the final list
MRIgtmSeg() done, t = 224.1820
Computing colortable
ERROR: cannot find match for subcortical segid 227
ERROR: mri_gtmseg --s 1122_test --usf 2 --o NEU_BN.gtmseg.mgz --apas
BN_apas+head.mgz --ctx-annot BN_Atlas.annot --ctab
/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_246_LUT.txt
--no-subseg-wm --no-keep-cc --no-keep-hypo
gtmseg exited with errors

Before I run gtmseg I used xcerebralseg --s 1122_test --m
aparc+BN_Atlas_subcotex.mgz --atlas
'/media/demenzbild/Studiendaten21/ADNI_Tau_study/fs_all_subjects/BN_Atlas_subcortex.gca'
 --o BN_apas+head.mgz

Any ideas on that?

Best,
Boris

Am Mo., 6. Jan. 2020 um 23:14 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> Are you sure you have permission to view that file?
>
> On 1/6/20 5:01 PM, Boris Rauchmann wrote:
> >  External Email - Use Caution
> >
> > I’m sure just double checked it. I don’t know what’s wrong here.
> >
> > Von meinem iPhone gesendet
> >
> >>> Am 06.01.2020 um 18:35 schrieb Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu>:
> >> This is not making any sense to me. Are you sure you are in
> >> $SUBJECTS_DIR/1122/mri when you run mri_aparc2aseg and are you sure that
> >> BN_Atlas_subcotex.mgz is in the same folder?
> >>
> >>> On 1/3/20 3:07 PM, Boris Rauchmann wrote:
> >>>
> >>>  External Email - Use Caution
> >>>
> >>> Thank you for testing it. As before I get the same error message.
> >>> Do you know what I´m doing wrong here?
> >>>
> >>> Best,
> >>> Boris
> >>>
> >>> MacBook-Pro:mri boris$ mri_aparc2aseg --s 1122 --volmask --aseg
> >>> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> >>> SUBJECTS_DIR /Users/boris/Desktop/MirLIND_test
> >>> subject 1122
> >>> outvol aparc+BN_Atlas_subcotex.mgz
> >>> useribbon 0
> >>> baseoffset 0
> >>> RipUnknown 0
> >>>
> >>> Reading lh white surface
> >>>   /Users/boris/Desktop/MirLIND_test/1122/surf/lh.white
> >>>
> >>> Reading lh pial surfac

Re: [Freesurfer] FsFast Question

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

Not directly as an external regressor. You would have to extract the 
info and create a waveform, one value for each TR in the external 
regressor file. You might also want to convolve it with a hemodynamic 
response function

On 1/8/20 11:15 AM, Swetara Joshi wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am new to fmri processing/FsFast and I had a question on creating 
> nuisance variables. Is it possible to set a block-design task fMRI 
> paradigm file as a nuisance variable, so that it can be inputted at a 
> .dat file for themkanalysis-sess command?
>
> Thank you!
>
> Best,
> Sweta
>
>
> *Sweta Joshi *
>
> *Research Assistant*
>
> Department of Neurology
>
> -
>
> GW Medical Faculty Associates
>
> George Washington University Hospital
>
> 2150 Pennsylvania Ave, NW, 9th Floor, Washington, DC 20037
>
> Office: 202.655.5888
>
> Email: sjo...@mfa.gwu.edu
>
>
>
> Confidentiality Note: This e-mail is intended only for the person or 
> entity to which it is addressed and may contain information that is 
> privileged, confidential or otherwise protected from disclosure. 
> Dissemination, distribution or copying of this e-mail or the 
> information herein by anyone other than the intended recipient, or an 
> employee or agent responsible for delivering the message to the 
> intended recipient, is prohibited. If you have received this e-mail in 
> error, please call (202) 741-3636 and destroy the original message and 
> all copies.
>
> ___
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[Freesurfer] Projection on fsaverage5

[Marina Fernández]

External Email - Use Caution

Hi Bruce,

Thanks for the quick response.

I found that the problem was the input. If I use the EPI that it is
coregistered to the T1 of Freesurfer instead of the EPI that it is also
normalized to the MNI space, it works and I can project the surface (that I
created with the command that I sent you) on fsaverage 5.

Could you confirm that the command has no errors?

mri_vol2surf --mov EPI.nii --reg register.dat --hemi [l/r]h --projfrac
0.5 --interp trilinear --trgsubject ico --icoorder 5 --o
EPI_surface.mgh


Best wishes,
Marina
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Re: [Freesurfer] Projection on fsaverage5

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

I think that should work, but I have not used the "ico" subject in a 
long time. It would be safer to use --trgsubject fsaverage. But you can 
also verify that they give the samme thing

On 1/8/20 12:12 PM, Marina Fernández wrote:
>
> External Email - Use Caution
>
> Hi Bruce,
>
> Thanks for the quick response.
>
> I found that the problem was the input. If I use the EPI that it is 
> coregistered to the T1 of Freesurfer instead of the EPI that it is 
> also normalized to the MNI space, it works and I can project the 
> surface (that I created with the command that I sent you) on fsaverage 5.
>
> Could you confirm that the command has no errors?
>
> mri_vol2surf --mov EPI.nii --reg register.dat --hemi [l/r]h --projfrac 0.5 
> --interp trilinear --trgsubject ico --icoorder 5 --o EPI_surface.mgh
> Best wishes,
> Marina
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca public permissions

[Hoopes, Andrew]

Hi Kostakis, sorry about that - should be fixed now!
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Kostakis Gkiatis 

Sent: Wednesday, January 8, 2020 5:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca 
public permissions

External Email - Use Caution

Dear Freesurfer experts,
I am trying to compile freesurfer from source. It is nicely performed
expect the "git annex get ." command which fails in these two files,
RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca.
I searched github's annex branch but no sign of the files. Do I have, as
public, the right permissions to download them? Can I find these two
files somewhere else?

Thank you in advance.
Yours sincerely,
Kostakis
--
Electrical and Computer Engineer
Phd Candidate in Brain Imaging
Medical Image Processing, Algorithms and Applications
National Technical University of Athens
9,Iroon Polytechneiou str.,
157 73 Zografou Campus,
Athens, GREECE
phone:+30 210 772 3577

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Re: [Freesurfer] Recommendation for CFT and CWT FreeSurfer analysis

[Martin Juneja]

External Email - Use Caution

Hi,

I have follow-up concerns. I also ran PALM as following to check my results:

palm -i y.mgh -s fsaverage/surf/lh.white
 fsaverage/surf/lh.white.avg.area.mgh -d X.csv -t C1.csv -m mask.mgh -o plm
-C 1.95996 -Cstat extent -twotail -n 5000

Interestingly, I get identical results (visually) between PALM (CFT = 0.05
i.e., 1.95996) and MCZ (CFT = 0.05 and CWT = 0.001). Outputs from both PALM
and MCZ overlap (looks like almost completely).

I have following few concerns (in addition to my previous questions from
previous email):
(1). Summary result file from MCZ gets automatically saved after running
mri_glmfit-sim. And, to save summary result file from PALM I ran
mri_binarize, mris_calc and mri_surfcluster commands (by looking at
previous discussions in FreeSurfer forum). However, summary file from MCZ
gives me two large clusters - with peaks within middle temporal and rostral
middle frontal, whereas summary file from PALM gives me two large clusters
of very similar size as of MCZ, but peaks within fusiform and lateral
orbitofrontal. It seems that both MCZ and PALM give two clusters based on
maxima using their other scheme - that's why although cluster sizes and
overall maps are similar but peaks differ - causing different names in
corresponding summary files despite the fact that I am using same
annotation file for both. Below I am attaching both the summary results
from PALM and MCZ. Could you help me in figuring out the way to generate
correct and reportable summary file? If both are correct in their own way,
I would really appreciate any explanation and preferable option here?

(2). If both of the above options are correct and as I get consistent
results from MCZ and PALM, then MCZ results clearly tell whether the
correlation is negative or positive (by looking at the cache*.summary and
cache*.cluster.mgh files. But I could not find a way from PALM results to
make sure the correlation is negative or positive. All the outputs e.g.,
*.fwep.mgz and *.tstat.mgz show positive maps always. Could you help in
finding the directionality of correlations from PALM option above?

(3). Again, as my results are consistent between MCZ and PALM, and for MCZ
I provide flag --2spaces (for Bonf. Correction of hemispheres) so I assume
that the above PALM command does not perform Bonf Correction, so I applied
Bonf Correction in mri_surfcluster command using the flag --bonferroni 2.
Could you please confirm is that's the correct way?

Thanks a lot for all your help.

Following is the summary file from PALM:

…..

…..

# SearchSpace_mm2 76467.1

# SearchSpace_vtx 149953

# Bonferroni 2

# Minimum Threshold 1e-12

# Maximum Threshold 0.05

# Threshold Signabs

# AdjustThreshWhenOneTail 1

# Area Threshold0 mm^2

# Overall max 0.998 at vertex 66

# Overall min 0 at vertex 0

# NClusters  2

# FixMNI = 0

#

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZNVtxsWghtVtx
  Annot

   10.042  11   2023.40-35.1  -23.3  -22.8   3523
147.97  fusiform

   20.044   9   1923.92-26.3   23.8   -6.0   3442
151.45  lateralorbitofrontal




Following is the summary file from MCZ:

…..

…..

# SearchSpace_mm2 76467.1

# SearchSpace_vtx 149953

# Bonferroni 2

# Minimum Threshold 1.3

# Maximum Threshold infinity

# Threshold Signabs

# AdjustThreshWhenOneTail 1

# CW PValue Threshold: 0.001

# Area Threshold0 mm^2

# CSD thresh  1.30

# CSD nreps1

# CSD simtype  null-z

# CSD contrast NA

# CSD confint  90.00

# Overall max 1.1597 at vertex 125047

# Overall min -4.53083 at vertex 110270

# NClusters  2

# FixMNI = 0

#

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow
  CWPHi   NVtxsWghtVtx   Annot

   1   -3.405  136882   2024.82-48.2   -1.6  -33.0  0.00020  0.0
0.00040   3526-6733.96  middletemporal

   2   -4.531  110270   1924.64-17.2   57.8  -13.3  0.00020  0.0
0.00040   3444-6888.13  rostralmiddlefrontal

On Mon, Jan 6, 2020 at 2:58 PM Martin Juneja  wrote:

> Hi,
>
> I am using Monte-Carlo simulations (for cortical thickness and volume -
> behavioral analysis) for clusterwise correction for multiple comparisons.
>
> My results are either significant at (i) CFT < 0.001 and CWT < 0.1 (i.e.,
> CWT = 0.07) (smoothing 12 mm) for cortical thickness-behavior analysis -
> with maxima at -4.3 (CFT)
> or (ii) CFT < 0.05 and CWT < 0.001 (i.e., CWT = 0.0002) (smoothing 10 mm)
> for cortical volume-behavior - with maxima at -4.53 (CFT)
>
> Both the clusters in (i) (lateral orbital frontal) and (ii) (rostral
> middle) are within the frontal cortex, but not overlapping !
> Also, although maxima is at (i) -4.3 and (ii) -4.53, still the clusters do
> not survive recommended thresholds suggested in
> https://www.ncbi.nlm.nih.gov/pubmed/29288131
> And the FPR in this paper at strong CWT (i..e, 0.001) and liberal CFT
> (i..e, 0.05) is not calculated.
>

[Freesurfer] funcroi-sess annotation issue

[Lewis, Lydia R.]

Hello Freesurfer Team,

I am running the fsfast analysis stream for resting state data and recently 
came across an issue with the funcroi-sess command. I originally used 
funcroi-config to configure the rois with the -annot aparc.a2009s $ROI flag to 
seed each of the regions from the 2009 annotation. But when I tried to do 
funcroi-sess I got the following error

ERROR reading 
$projectdir/sess01/rest/lh_G_and_S_frontomargin.fc/tmp.funcroi-sess.lh.G_and_S_frontomargin/label/lh.lh_G_and_S_frontomargin.label

It seems like this is because first command (mri_annotation2label) generates 
labels with slightly different names, such as 
$projectdir/sess01/rest/lh_G_and_S_frontomargin.fc/tmp.funcroi-sess.G&S_frontomargin.fc/label/lh.G&S_frontomargin.label.
 For instance, if I edit the config file to:

roiname lh.G_and_S_frontomargin
annot aparc.a2009s G&S_frontomargin
fillthresh 0
analysis lh_G_and_S_frontomargin.fc

the funcroi-sess command works fine.

As a solution, I edited my script to change the annotations to 1) remove the 
hemisphere from the prefix, and 2) replace G_and_S with G&S. With these 
changes, the funcroi-sess command seems to be working correctly.

I just wanted to get some feedback on whether this was a valid solution, or if 
this error is occurring because of some other larger issue that I will need to 
fix/be aware of. For reference I am using the stable6 version of freesurfer.

Thanks for your time,
Lydia Lewis
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[Freesurfer] single-trial analysis of BOLD data in FSFAST

[Katsumi, Yuta]

Dear Doug,

I would like to perform GLM on a trial-by-trial basis in FSFAST. That is, I'm 
interested in obtaining beta estimates per trial and using them as input for 
group-level analyses of activation patterns (e.g., MVPA) or functional 
connectivity (e.g., beta series correlations). I've done this in the past using 
SPM to analyze data in volume space, and now would like to take a similar 
approach using FSFAST to analyze data in surface space. Would you please advise 
how I might be able to implement this? Thanks in advance for your input.

Best,
Yuta
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Re: [Freesurfer] RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca public permissions

[Kostakis Gkiatis]

External Email - Use Caution

Dear Andrew,
Thank you for your quick response.
It works perfectly now.

Kostakis
---
Electrical and Computer Engineer
Phd Candidate in Brain Imaging
Medical Image Processing, Algorithms and Applications
National Technical University of Athens
9,Iroon Polytechneiou str.,
157 73 Zografou Campus,
Athens, GREECE
phone:+30 210 772 3577


 Original Message 
Subject: Re: [Freesurfer] RB_all_2020-01-02.gca and 
RB_all_withskull_2020_01_02.gca public permissions
Date: 08/01/2020 21:31
 From: "Hoopes, Andrew" 
To: "freesurfer@nmr.mgh.harvard.edu" 

Hi Kostakis, sorry about that - should be fixed now!
Andrew


 From: freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Kostakis Gkiatis

Sent: Wednesday, January 8, 2020 5:53 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] RB_all_2020-01-02.gca and
RB_all_withskull_2020_01_02.gca public permissions

 External Email - Use Caution

Dear Freesurfer experts,
I am trying to compile freesurfer from source. It is nicely performed
expect the "git annex get ." command which fails in these two files,
RB_all_2020-01-02.gca and RB_all_withskull_2020_01_02.gca.
I searched github's annex branch but no sign of the files. Do I have, as
public, the right permissions to download them? Can I find these two
files somewhere else?

Thank you in advance.
Yours sincerely,
Kostakis
--
Electrical and Computer Engineer
Phd Candidate in Brain Imaging
Medical Image Processing, Algorithms and Applications
National Technical University of Athens
9,Iroon Polytechneiou str.,
157 73 Zografou Campus,
Athens, GREECE
phone:+30 210 772 3577

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[Freesurfer] mri_glmfit with flag -pvr

[Vicky Shi]

External Email - Use Caution

Dear Freesurfer team,

I am running the glm analysis on CBF maps. I have two class and I want to
see the group difference regressing out the cortex thickness. I know that I
can add the average cortical thickness as one covariable in FSDG file.
However, I think it might worth trying to do this with GLM by using a per
vertex regressor (thickness).

My fsgd file is like below:

Class Patient
Class CTL
INPUT subj1 Patient
INPUT subj2 CTL


My command is below:
mri_glmfit --y lh.fsaverage.cbf.sm10.mgz --fsgd fsgd.txt --C contrast.mtx
--glmdir lh.output.glmdir --surf fsaverage lh --pvr lh.thickness.sm10.mgz

My contrast matrix is -1 1 0.

I am wondering if what I do is correct or not. Does it make sense or I
should use the mean thickness as regressor?

Thank you for your time!

Best regards,
Vicky
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