Dear Douglas ,

I used 

mri_vol2surf \
  --mov /path/to/ROI5.nii \
  --reg TT_avg152T1_to_fsaverage.dat \
  --projdist-max 0 1 0.1 \
  --interp nearest \
  --hemi lh \
  --out lh.fsaverage.ROI5.mgh \
  --reshape

And I got lh.thickness.fseaverage.mgh from the normal pipeline using recon-all. It’s the patient specific thickness average. 

Elodie 




On Mar 8, 2017, at 7:27 PM, freesurfer-request@nmr.mgh.harvard.edu wrote:

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Today's Topics:

  1. Re: Error viewing corrected results (Antonin Skoch)
  2. Re: mri_concat pet images into 1 template image (Douglas Greve)
  3. Re: mri_concat pet images into 1 template image (Shane S)
  4. Re: Error viewing corrected results (Sahil Bajaj)
  5. Issue with mri_segstats to extract cortical thickness from a
     volume ROI (Elodie Boudes)
  6. mri_label2vol error: could not scan # of lines from label
     file (Burks, Joshua D (HSC))
  7. Re: Yet another freeview coordinates question (Peled, Noam)
  8. Results from R to Freesurfer (Dorian P.)


----------------------------------------------------------------------

Message: 1
Date: Wed, 8 Mar 2017 23:05:07 +0100
From: Antonin Skoch <ansk@ikem.cz>
Subject: Re: [Freesurfer] Error viewing corrected results
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <2951470448-17194@posta.medicon.cz>
Content-Type: text/plain; charset="utf-8"

Dear Sahil,

If you used -logp as Anderson suggested, you should set your min to 1.3 to threshold your *_clustere_tstat_fwep map and see the clusters.

What is the value of *_clustere_tstat_fwep in the region of the big cluster seen at thresholded map *dpv_tstat.mgz ?? This should correspond to your -log10(p) of your cluster.

I personally did not use -logp and use the mri_surfcluster for the reporting of the clusters, as I wrote in previous mail here:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html

But it is only matter of personal preference.

And, beware, that the LGI is very smooth measure, therefore also rather big cluster can be insignificant after FWER correction.

Antonin



Hi Antonin,

Here, I am sending you more information:

(1). I used following command:
palm -i lh.Behav_LGI.10.mgh -s fsaverage/surf/lh.white
fsaverage/surf/lh.white.avg.area.mgh -d Xg_Behav.csv -t Contrast_Behav.csv
-m lh.Behav_LGI.glmdir/mask.mgh -o Results_Left -Cstat extent -C 1.95
-approx tail -n 500 -nouncorrected -logp

(2). Somehow, view of *_clustere_tstat_fwep is single colored, thresholded
0 (min) and 1(max), which seems suspicious. Please find it attached.

(3). Data showed in screen shot 1 is just partial correlation coefficient
(PCC, limiting between 0.30-0.35), obtained after running glm_fit command
and saved in glm directory.

(4). *_clustere_tstat_fwep is attached here in this email.

(5). If I load *dpv_tstat.mgz and threshold it between 1.3 (p = 0.05) and 2
(max), I get the map attached 2nd in attached figure. I am not sure
how to "threshold
it by your cluster-forming threshold (I suppose that you should correctly
convert z value to t-value), to see your initial clusters after
thresholding".

Thanks a lot Antonin.
Sahil



On Wed, Mar 8, 2017 at 2:06 PM, Antonin Skoch <ansk@ikem.cz> wrote:

Dear Sahil,

could you send the full command-line and unthresholded view of
*_clustere_tstat_fwep ?

How the data showed in screenshot 1 were produced?

How are the actual p-values of your clusters in *_clustere_tstat_fwep?

You can also use -saveglm and inspect the files containing values of GLM
fit.
You can load the *dpv_tstat.mgz file and threshold it by your
cluster-forming threshold (I suppose that you should correctly convert z
value to t-value), to see your initial clusters after thresholding.

Regards,

Antonin



Thanks a lot Anderson and Antonin, that's really useful.

Actually, I am having trouble in interpreting the results. Could you
please
share any document explaining all these tests/outputs and their
interpretation in simple terms?

Here I am attaching a screen shot: (1) Simple partial correlations (I
adjusted the color bar between 0.30 and 0.35 to visualize the high
correlation coefficients, which is ~0.35) and (2) Results I get when I
used cluster
extent stats: *dpv_tstat
But I do not see any significant clusters when I view
*_clustere_tstat_fwep, *_dpv_tstat_fwep, which is very unexpected in my
data set.

So basically I really doubt if I am running the stats correctly because
PCC
looks high at that big cluster (shown in PCC in attached screen shot).

Could you please suggest if there is any alternative (less stronger) stat
flag I can use here while running PALM command?

I would be more than happy sharing any required files to interpret the
results.

Thanks.

On Wed, Mar 8, 2017 at 10:20 AM, Sahil Bajaj <sahil.brain@gmail.com>
wrote:

Thanks a lot Anderson and Antonin, that's really useful.

Actually, I am having trouble in interpreting the results. Could you
please share any document explaining all these tests/outputs and their
interpretation in simple terms?

Here I am attaching two screen shots: (1) Results I get when I used
cluster
extent stats: *dpv_tstat and (2). Simple partial correlations (I
adjusted
the color bar between 0.30 and 0.35 to visualize the high correlation
coefficients, which is ~0.35).
I do not see any significant clusters when I view *_clustere_tstat_fwep,
*_dpv_tstat_fwep, which is very unexpected in my data set.

So basically I really doubt if I am running the stats correctly because
PCC looks high at that big cluster (shown in PCC in attached screen
shot).

Could you please suggest if there is any alternative (less stronger)
stat
flag I can use here while running PALM command?

I would be more than happy sharing any required files to interpret the
results.

Thanks.

On Wed, Mar 8, 2017 at 9:27 AM, Martin Juneja <mj70481@gmail.com>
wrote:

Hi Antonin and Anderson,

That's wonderful ! I am able to run PALM now, without any problem.

Thank you so much for your help and time, I really appreciate that.

Best,
MJ



On Wed, Mar 8, 2017 at 6:30 AM, Anderson M. Winkler <
winkler@fmrib.ox.ac.uk> wrote:

Hi all,

That's exactly as Antonin says -- I have very little to add :-)

Only a few suggestions:

- With surfaces, both cluster and TFCE statistics tend to be slow.
Consider using the tail approximation ("-approx tail -n 500
-nouncorrected")

- Include -logp, so that the p-values are in log-10 scale. Significant
p-values are then those above 1.3 (i.e., -log10(0.05). This will help
to
make the figures nicer later.

All the best,

Anderson



On 8 March 2017 at 00:19, Antonin Skoch <ansk@ikem.cz> wrote:

Dear Sahil,

I suppose, for qcache 1.3 the equivalent cluster-forming threshold
z-value is

two-tailed test:
qnorm(1-10^-1.3/2)=1.958949

for one-tailed test:
qnorm(1-10^-1.3)=1.643704

(qnorm is R function call for quantile function of normal
distribution,
you can compute this by using other methods or use statistical
z-tables)

And, the directionality of the hypothesis is I suppose specified by
the
sign of your contrast vector, as I wrote in my previous mail.

As for the output files, you can look at the documentation:

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide#Output_files

For example, if you are looking for the p-values, used cluster extent
inference and used t-contrast, the file with FWER-corrected p-values
would
be something like

output_basename_clustere_tstat_fwep.mgz

Antonin




Hello Martin and Antonin,

I was following this conversation very closely to understand how to
use
PALM in FreeSurfer.

Can any of you please confirm in case I am interested in checking
correlation between gyrification index (LGI) and behavioral measure
using
two tailed, p < 0.05:
Step 1: I used --cache 1.3
Step 2: Because (1-10^-1.3)= 0.95, so I will have to use -C 0.95 in
palm
command

Could you please confirm if thats correct and the output *_tstat.mgz
is the
final two-tailed corrected significant correlation map between LGI
and
behavioral data?

Thanks a lot for this wonderful discussion.
Sahil

PS: For one-tailed: it will be -C -0.95 in palm command, correct?



On Tue, Mar 7, 2017 at 3:48 PM, Antonin Skoch <a...@ikem.cz> wrote:

Dear Martin,

after -s option, there have to be 2 arguments, as I specified in my
previous
mail:

-s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh

And beware that -C has to have negative sign, if your hypothesis is
one-tailed negative.

Antonin



Hi Antonin,

Thank you so much for this detailed explanation, that's really
useful.

Following your instructions, I ran:

palm -i lh.MEQ_LGI.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh
-d
check.csv -t Contrast_MEQ.csv -n 5000 -m lh.MEQ_LGI.glmdir/mask.mgh
-o
myresults -Cstat extent -C 3.719016

but I am getting following error:

Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with the
following
options:
-i lh.MEQ_LGI.10.mgh
-s fsaverage/surf/lh.white.avg.area.mgh
-d check.csv
-t Contrast_MEQ.csv
-n 5000
-m lh.MEQ_LGI.glmdir/mask.mgh
-o myresults
-Cstat extent
-C 3.719016
Loading surface 1/1: fsaverage/surf/lh.white.avg.area.mgh
Reading input 1/1: lh.MEQ_LGI.10.mgh

Struct contents reference from a non-struct array object.

Error in palm_takeargs (line 1632)
? ? ? ? ? ? if any(size(plm.srf{s}.data.vtx,
1) == ...

Error in palm_core (line 33)
[opts,plm] = palm_takeargs(varargin{:});

Error in palm (line 81)
palm_core(varargin{:});

Could you please help me in resolving this error?

Thanks much.

On Tue, Mar 7, 2017 at 2:55 PM, Antonin Skoch <a...@ikem.cz>
wrote:

Dear Martin,

input -i input file is

lh.MEQ_LGI.10.mgh file in your glmdir directory (for left
hemisphere).

As you could read in following messages in the referenced thread
in FSL
discussion forum, cluster-forming threshold need to be specified
in z, not
in t.

Therefore, you would have to select cluster forming threshold and
specify
it as a z score.

I think that your z-score for your original mri_glmfit-sim
commandline
argument

--cache 4 neg

will be ?-qnorm(1-10^-4)=-3.719016. (I am not perfectly sure
since I never
tried negative one-side hypothesis testing in PALM).

You could also use other statistics, such as cluster mass, or
TFCE. See
PALM user guide.

Do not include -pmethodp none and -pmethodr none, since you would
need the
partitioning due your non-orthogonal design matrix.

?h.white.avg.area.mgh file (which you will find under fsaverage
directory)
goes as second argument after -s option.

Therefore I suppose the commandline for cluster extent inference
with
cluster forming threshold p=0.0001, negative one-sided
hypothesis, left
hemisphere, will be hopefully something like

palm
-i y.mgh
-s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh
-d Xg.csv
-t your_contrasts.csv
-n number_of_permutations
-m mask.mgh
-o output_basename
-Cstat extent
-C -3.719016
-saveglm
-savedof
-savemetrics

The last 3 commandline options are only for diagnostical
purposes.

The output is surface overlay you can visualize in freeview.

I use following code snippet for the reporting significant
clusters in MNI
coordinates:

# PALM output cluster extent p maps have 1 outside cluster -
problem with
mri_surfcluster and also for display in freeView
#here we set values 1 to 0 in pmaps.
#done by binarizing and subtracting
if [[ $# -ne 2 ]]; then
echo "get cluster summary of PALM statistics. Expecting 2
arguments: 1-
input p-map, 2- hemisphere (lh/rh)"
exit
fi
mri_binarize --i $1 --min 1 --o p_bin.mgz
mris_calc --output ${1%%.mgz}_filtered.mgz $1 sub p_bin.mgz
mri_surfcluster --in ${1%%.mgz}_filtered.mgz --subject fsaverage
--hemi $2
--surf white --annot aparc --thmin 0.000000001 --thmax 0.05
--mask mask.mgh
--sum ${1%%.mgz}_cluster.summary --nofixmni
rm p_bin.mgz

They are not Bonferroni-corrected for 2 hemispheres (--2spaces).

Regarding your design and contrast:

Design has to be matrix of values. You can use qdec to produce
Xg.dat file
with design matrix, then rename it to Xg.csv to be correctly
readable by
PALM.

Regards,

Antonin





Hi Antonin,

As you suggested in discussion forum, I tried to run following
command
after mri_glmfit:

palm -s fsaverage/surf/lh.white -n 10000 -m mask.mgh -Cstat
extent -C
1.974975 -pmethodp none -pmethodr none -twotail -d Design_MEQ.txt
-t
Contrast_MEQ.txt

Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with the
following
options:

-s fsaverage/surf/lh.white

-n 10000

-m mask.mgh

-Cstat extent

-C 1.974975

-pmethodp none

-pmethodr none

-twotail

-d Design.txt

-t Contrast.txt

Found FSL in /usr/share/fsl/5.0

Found FreeSurfer in /usr/local/freesurfer

Found SPM in /usr/local/spm12

Error using palm_takeargs (line 1141)

Missing input data (missing "-i").

Error in palm_core (line 33)

[opts,plm] = palm_takeargs(varargin{:});

Error in palm (line 81)

palm_core(varargin{:});

Looks like error is because its missing -i input here, I am not
sure what's
input file here?

Also, I am trying to correlate LGI versus behavioral score,
regressing out
the effect of sex and age. So I just wanted to confirm if my
design.txt and
contrast.txt files are correct here. Please find both following:

Design file (Variables Behav, Age) as following:

S001 Male 60 36

S003 Female 73 29

S004 Male 48 39

.......so on......

Contrast file as following:
0 0 0.5 0.5 0 0 (same as *.mtx file used for glm_fit)

Thank you so much for your help and time.

On Tue, Mar 7, 2017 at 10:49 AM, Martin Juneja <mj70...@gmail.com>
wrote:

Hi Antonin,

Thanks a lot for your reply.

Somehow, in the link you sent, I could not find any response to
your
email. But I can see your email to Anderson and command line
parameters.

As I am not an expert in using FreeSurfer, so would it be
possible for you
to share detailed step-by-step guide and PALM command after I
run
mri_glmfit
command and how and where to include '?h.white.avg.area.mgh'
file?

I would really appreciate any help.

On Mon, Mar 6, 2017 at 4:28 PM, Antonin Skoch <a...@ikem.cz>
wrote:

Dear Martin,

I think yes, you can use PALM with FreeSurfer surfaces, see my
conversation with Anderson on FSL list:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L=FSL



&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=239088

but beware not to forget to include average the vertex area
(?h.white.avg.area.mgh) file.

Antonin


If you don't have an orthogonal design, then you can't use
mri_glmfit-sim. I think you can use PALM:

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM

I have not tried it yet.

Anderson, can you use PALM with surfaces?






On 03/06/2017 05:23 PM, Martin Juneja wrote:
Hi Dr. Greve,

I tried to run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir
--sim perm
1000 3 permcsd --sim-sign abs --cwpvalthresh .05
It gives error that ERROR: design matrix is not orthogonal,
cannot be
used with permutation.

But when I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir
--sim perm
1000 3 permcsd --sim-sign abs --cwpvalthresh .05
--perm-force, it
works.

I am not sure whether I will have to make the design matrix
orthogonal. If so, could you please tell me how that can be
done?

Or using --perm-force should be fine?

Thanks.

On Mon, Mar 6, 2017 at 1:58 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu
<gr...@nmr.mgh.harvard.edu>
<gr...@nmr.mgh.harvard.edu>
<gr...@nmr.mgh.harvard.edu>
<gr...@nmr.mgh.harvard.edu>>> wrote:

? ? This is a problem with using LGI in that it is already
extremely
? ? smooth
? ? that the smoothness exceeds the limit of the look up
table that we
? ? supply. I ?recommend that you not use a gaussian-based
correction
for
? ? LGI. Instead, use permutation (see mri_glmfit-sim
--help).



? ? On 03/06/2017 01:36 PM, Martin Juneja wrote:
? ? > Hello everyone,
? ? >
? ? > I am trying to extract clusters showing significant
correlation
? ? > between LGI and a behavioral measure. I am able to
extract PCC
and
? ? > sig.mgh but at the last step when I try to run
simulation command
to
? ? > view corrected results and I run:
? ? >
? ? > mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4
neg --cwp
0.05
? ? > --2spaces
? ? >
? ? > I get following error:
? ? >
? ? > ERROR: cannot find
? ? >

/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/
cortex/fwhm35/neg/th40/mc-z.csd
? ? >
? ? > But I can see mc-z.csd file in fwhm30 etc.
? ? >
? ? > Full message on terminal window is attached following.
? ? >
? ? > Any help would be really appreciated.
? ? >
? ? > ----- Full message ----
? ? >
? ? > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd
MEQ.fsgd
? ? dods --C
? ? > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir
? ? lh.MEQ_LGI.glmdir
? ? >
? ? > WARNING: unrecognized mri_glmfit cmd option
mri_glmfit.bin
? ? >
? ? > SURFACE: fsaverage lh
? ? >
? ? > log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log

? ? >
? ? > /usr/local/freesurfer/bin/mri_glmfit-sim
? ? >
? ? > --glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05
--2spaces
? ? >
? ? > $Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve
Exp $
? ? >
? ? > Mon Mar ?6 11:11:13 MST 2017
? ? >
? ? > setenv SUBJECTS_DIR
? ? > /data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll

? ? >
? ? > FREESURFER_HOME /usr/local/freesurfer
? ? >
? ? > Original mri_glmfit command line:
? ? >
? ? > cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd
MEQ.fsgd
? ? dods --C
? ? > Corr-MEQ-cor.mtx --surf fsaverage lh --cortex --glmdir
? ? lh.MEQ_LGI.glmdir
? ? >
? ? > DoSim = 0
? ? >
? ? > UseCache = 1
? ? >
? ? > DoPoll = 0
? ? >
? ? > DoPBSubmit = 0
? ? >
? ? > DoBackground = 0
? ? >
? ? > DiagCluster = 0
? ? >
? ? > gd2mtx = dods
? ? >
? ? > fwhm = 35.073391
? ? >
? ? > ERROR: cannot find
? ? >

/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/
cortex/fwhm35/neg/th40/mc-z.csd
? ? >
? ? >


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Message: 2
Date: Wed, 8 Mar 2017 17:30:40 -0500
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_concat pet images into 1 template image
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <fd5d66bf-1067-1125-f8cf-9a1e713c9c9c@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

No, the template is a within subject template used for registration. If
your pet data only has one frame (eg, FDG SUV), then you don't need to
run mri_convert or mri_concat, just use your pet image as the template


On 3/8/17 11:11 AM, Shane S wrote:
Hello Freesurfer,

I have 3 PET images per individual. I am learning PetSurfer based on
the Greve et al., 2014 paper.

On the PetSurfer link, there are 2 methods.

mri_convert pet.nii.gz ?frame frameno template.nii.gz
or
mri_concat pet.nii.gz --mean ?0 template.nii.gz

What are the differences? My files are listed as subject123_a.nii.gz,
subject123_b.nii.gz, subject123_c.nii.gz

Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz,
subject123_c.nii.gz ?mean ?o template.nii.gz? correct?

Thank you for helping.

Best Wishes,

S
--
Shane Schofield


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

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Message: 3
Date: Wed, 8 Mar 2017 22:33:48 +0000
From: Shane S <shane.schofield@yahoo.com>
Subject: Re: [Freesurfer] mri_concat pet images into 1 template image
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <etPan.58c086cc.19a42184.2b9@yahoo.com>
Content-Type: text/plain; charset="utf-8"

Dear Doug,

My PET data is 3 x 5 minute acquisitions. Each subject has?
subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz and I am supposed to align and average them.

Please advise.

Thanks!

--?
Shane Schofield

On 8 March 2017 at 22:31:06, Douglas Greve (greve@nmr.mgh.harvard.edu) wrote:

No, the template is a within subject template used for registration. If your pet data only has one frame (eg, FDG SUV), then you don't need to run mri_convert or mri_concat, just use your pet image as the template


On 3/8/17 11:11 AM, Shane S wrote:
Hello Freesurfer,

I have 3 PET images per individual. I am learning PetSurfer based on the Greve et al., 2014 paper.?

On the PetSurfer link, there are 2 methods.

mri_convert pet.nii.gz ?frame frameno template.nii.gz?
or
mri_concat pet.nii.gz --mean ?0 template.nii.gz

What are the differences? My files are listed as subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz

Is "mri_concat subject123_a.nii.gz, subject123_b.nii.gz, subject123_c.nii.gz ?mean ?o template.nii.gz? correct?

Thank you for helping.

Best Wishes,

S
--?
Shane Schofield


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

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Message: 4
Date: Wed, 8 Mar 2017 16:25:06 -0700
From: Sahil Bajaj <sahil.brain@gmail.com>
Subject: Re: [Freesurfer] Error viewing corrected results
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAAvfsVj7FM0ogSTO-secc1nzFLiZE9yLjq2JLkJ=cdRJ4ou=CA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear Antonin,

Setting minimum to 1.3 for *_clustere_tstat_fwep doesn't show any
significant cluster and similarly thresholded map *dpv_tstat.mgz also
doesn't show anything at -log10(0.05) = 1.3. As you said, it seems like
even though there is big cluster but after FWER correction, the
significance goes away. Actually, even when I removed -logp, I still do not
see any significant cluster.

Next, I tried to use mri_surfcluster using following three commands
following instructions from the link you sent:

mri_binarize --i Results_Left_clustere_tstat_fwep.mgz --min 1 --o p_bin.mgz

mris_calc --output pmap_filter.mgz Results_Left_clustere_tstat_fwep.mgz sub
p_bin.mgz

mri_surfcluster --in pmap_filter.mgz --subject fsaverage --hemi lh --surf
white --annot aparc.a2009s --thmin 0.00000001 --thmax 0.05 --mask
glmdir/mask.mgh --sum summary --nofixmni

This gives me 'zero' cluster in the summary file.

If the above steps are correct, would you conclude that the LGI results are
not significant and un-reportable for publication purpose and I should give
a try to thickness, volume and area maps?

Thanks you so much Antonin for all your help.
Sahil



On Wed, Mar 8, 2017 at 3:05 PM, Antonin Skoch <ansk@ikem.cz> wrote:

Dear Sahil,

If you used -logp as Anderson suggested, you should set your min to 1.3 to
threshold your *_clustere_tstat_fwep map and see the clusters.

What is the value of *_clustere_tstat_fwep in the region of the big
cluster seen at thresholded map *dpv_tstat.mgz ?  This should correspond to
your -log10(p) of your cluster.

I personally did not use -logp and use the mri_surfcluster for the
reporting of the clusters, as I wrote in previous mail here:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html

But it is only matter of personal preference.

And, beware, that the LGI is very smooth measure, therefore also rather
big cluster can be insignificant after FWER correction.

Antonin




Hi Antonin,

Here, I am sending you more information:

(1). I used following command:
palm -i lh.Behav_LGI.10.mgh -s fsaverage/surf/lh.white
fsaverage/surf/lh.white.avg.area.mgh -d Xg_Behav.csv -t
Contrast_Behav.csv
-m lh.Behav_LGI.glmdir/mask.mgh -o Results_Left -Cstat extent -C 1.95
-approx tail -n 500 -nouncorrected -logp

(2). Somehow, view of *_clustere_tstat_fwep is single colored, thresholded
0 (min) and 1(max), which seems suspicious. Please find it attached.

(3). Data showed in screen shot 1 is just partial correlation coefficient
(PCC, limiting between 0.30-0.35), obtained after running glm_fit command
and saved in glm directory.

(4). *_clustere_tstat_fwep is attached here in this email.

(5). If I load *dpv_tstat.mgz and threshold it between 1.3 (p = 0.05) and
2
(max), I get the map attached 2nd in attached figure. I am not sure
how to "threshold
it by your cluster-forming threshold (I suppose that you should correctly
convert z value to t-value), to see your initial clusters after
thresholding".

Thanks a lot Antonin.
Sahil



On Wed, Mar 8, 2017 at 2:06 PM, Antonin Skoch <ansk@ikem.cz> wrote:

Dear Sahil,

could you send the full command-line and unthresholded view of
*_clustere_tstat_fwep ?

How the data showed in screenshot 1 were produced?

How are the actual p-values of your clusters in *_clustere_tstat_fwep?

You can also use -saveglm and inspect the files containing values of GLM
fit.
You can load the *dpv_tstat.mgz file and threshold it by your
cluster-forming threshold (I suppose that you should correctly convert z
value to t-value), to see your initial clusters after thresholding.

Regards,

Antonin



Thanks a lot Anderson and Antonin, that's really useful.

Actually, I am having trouble in interpreting the results. Could you
please
share any document explaining all these tests/outputs and their
interpretation in simple terms?

Here I am attaching a screen shot: (1) Simple partial correlations (I
adjusted the color bar between 0.30 and 0.35 to visualize the high
correlation coefficients, which is ~0.35) and (2) Results I get when I
used cluster
extent stats: *dpv_tstat
But I do not see any significant clusters when I view
*_clustere_tstat_fwep, *_dpv_tstat_fwep, which is very unexpected in my
data set.

So basically I really doubt if I am running the stats correctly because
PCC
looks high at that big cluster (shown in PCC in attached screen shot).

Could you please suggest if there is any alternative (less stronger)
stat
flag I can use here while running PALM command?

I would be more than happy sharing any required files to interpret the
results.

Thanks.

On Wed, Mar 8, 2017 at 10:20 AM, Sahil Bajaj <sahil.brain@gmail.com>
wrote:

Thanks a lot Anderson and Antonin, that's really useful.

Actually, I am having trouble in interpreting the results. Could you
please share any document explaining all these tests/outputs and their
interpretation in simple terms?

Here I am attaching two screen shots: (1) Results I get when I used
cluster
extent stats: *dpv_tstat and (2). Simple partial correlations (I
adjusted
the color bar between 0.30 and 0.35 to visualize the high correlation
coefficients, which is ~0.35).
I do not see any significant clusters when I view
*_clustere_tstat_fwep,
*_dpv_tstat_fwep, which is very unexpected in my data set.

So basically I really doubt if I am running the stats correctly
because
PCC looks high at that big cluster (shown in PCC in attached screen
shot).

Could you please suggest if there is any alternative (less stronger)
stat
flag I can use here while running PALM command?

I would be more than happy sharing any required files to interpret the
results.

Thanks.

On Wed, Mar 8, 2017 at 9:27 AM, Martin Juneja <mj70481@gmail.com>
wrote:

Hi Antonin and Anderson,

That's wonderful ! I am able to run PALM now, without any problem.

Thank you so much for your help and time, I really appreciate that.

Best,
MJ



On Wed, Mar 8, 2017 at 6:30 AM, Anderson M. Winkler <
winkler@fmrib.ox.ac.uk> wrote:

Hi all,

That's exactly as Antonin says -- I have very little to add :-)

Only a few suggestions:

- With surfaces, both cluster and TFCE statistics tend to be slow.
Consider using the tail approximation ("-approx tail -n 500
-nouncorrected")

- Include -logp, so that the p-values are in log-10 scale.
Significant
p-values are then those above 1.3 (i.e., -log10(0.05). This will
help
to
make the figures nicer later.

All the best,

Anderson



On 8 March 2017 at 00:19, Antonin Skoch <ansk@ikem.cz> wrote:

Dear Sahil,

I suppose, for qcache 1.3 the equivalent cluster-forming threshold
z-value is

two-tailed test:
qnorm(1-10^-1.3/2)=1.958949

for one-tailed test:
qnorm(1-10^-1.3)=1.643704

(qnorm is R function call for quantile function of normal
distribution,
you can compute this by using other methods or use statistical
z-tables)

And, the directionality of the hypothesis is I suppose specified by
the
sign of your contrast vector, as I wrote in my previous mail.

As for the output files, you can look at the documentation:

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/UserGuide#Output_files

For example, if you are looking for the p-values, used cluster
extent
inference and used t-contrast, the file with FWER-corrected
p-values
would
be something like

output_basename_clustere_tstat_fwep.mgz

Antonin




Hello Martin and Antonin,

I was following this conversation very closely to understand how to
use
PALM in FreeSurfer.

Can any of you please confirm in case I am interested in checking
correlation between gyrification index (LGI) and behavioral measure
using
two tailed, p < 0.05:
Step 1: I used --cache 1.3
Step 2: Because (1-10^-1.3)= 0.95, so I will have to use -C 0.95 in
palm
command

Could you please confirm if thats correct and the output
*_tstat.mgz
is the
final two-tailed corrected significant correlation map between LGI
and
behavioral data?

Thanks a lot for this wonderful discussion.
Sahil

PS: For one-tailed: it will be -C -0.95 in palm command, correct?



On Tue, Mar 7, 2017 at 3:48 PM, Antonin Skoch <a...@ikem.cz>
wrote:

Dear Martin,

after -s option, there have to be 2 arguments, as I specified in
my
previous
mail:

-s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh

And beware that -C has to have negative sign, if your hypothesis
is
one-tailed negative.

Antonin



Hi Antonin,

Thank you so much for this detailed explanation, that's really
useful.

Following your instructions, I ran:

palm -i lh.MEQ_LGI.10.mgh -s fsaverage/surf/lh.white.avg.area.mgh

-d
check.csv -t Contrast_MEQ.csv -n 5000 -m
lh.MEQ_LGI.glmdir/mask.mgh
-o
myresults -Cstat extent -C 3.719016

but I am getting following error:

Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with the
following
options:
-i lh.MEQ_LGI.10.mgh
-s fsaverage/surf/lh.white.avg.area.mgh
-d check.csv
-t Contrast_MEQ.csv
-n 5000
-m lh.MEQ_LGI.glmdir/mask.mgh
-o myresults
-Cstat extent
-C 3.719016
Loading surface 1/1: fsaverage/surf/lh.white.avg.area.mgh
Reading input 1/1: lh.MEQ_LGI.10.mgh

Struct contents reference from a non-struct array object.

Error in palm_takeargs (line 1632)
           if any(size(plm.srf{s}.data.vtx,
1) == ...

Error in palm_core (line 33)
[opts,plm] = palm_takeargs(varargin{:});

Error in palm (line 81)
palm_core(varargin{:});

Could you please help me in resolving this error?

Thanks much.

On Tue, Mar 7, 2017 at 2:55 PM, Antonin Skoch <a...@ikem.cz>
wrote:

Dear Martin,

input -i input file is

lh.MEQ_LGI.10.mgh file in your glmdir directory (for left
hemisphere).

As you could read in following messages in the referenced
thread
in FSL
discussion forum, cluster-forming threshold need to be
specified
in z, not
in t.

Therefore, you would have to select cluster forming threshold
and
specify
it as a z score.

I think that your z-score for your original mri_glmfit-sim
commandline
argument

--cache 4 neg

will be  -qnorm(1-10^-4)=-3.719016. (I am not perfectly sure
since I never
tried negative one-side hypothesis testing in PALM).

You could also use other statistics, such as cluster mass, or
TFCE. See
PALM user guide.

Do not include -pmethodp none and -pmethodr none, since you
would
need the
partitioning due your non-orthogonal design matrix.

?h.white.avg.area.mgh file (which you will find under fsaverage
directory)
goes as second argument after -s option.

Therefore I suppose the commandline for cluster extent
inference
with
cluster forming threshold p=0.0001, negative one-sided
hypothesis, left
hemisphere, will be hopefully something like

palm
-i y.mgh
-s fsaverage/surf/lh.white fsaverage/surf/lh.white.avg.area.mgh

-d Xg.csv
-t your_contrasts.csv
-n number_of_permutations
-m mask.mgh
-o output_basename
-Cstat extent
-C -3.719016
-saveglm
-savedof
-savemetrics

The last 3 commandline options are only for diagnostical
purposes.

The output is surface overlay you can visualize in freeview.

I use following code snippet for the reporting significant
clusters in MNI
coordinates:

# PALM output cluster extent p maps have 1 outside cluster -
problem with
mri_surfcluster and also for display in freeView
#here we set values 1 to 0 in pmaps.
#done by binarizing and subtracting
if [[ $# -ne 2 ]]; then
echo "get cluster summary of PALM statistics. Expecting 2
arguments: 1-
input p-map, 2- hemisphere (lh/rh)"
exit
fi
mri_binarize --i $1 --min 1 --o p_bin.mgz
mris_calc --output ${1%%.mgz}_filtered.mgz $1 sub p_bin.mgz
mri_surfcluster --in ${1%%.mgz}_filtered.mgz --subject
fsaverage
--hemi $2
--surf white --annot aparc --thmin 0.000000001 --thmax 0.05
--mask mask.mgh
--sum ${1%%.mgz}_cluster.summary --nofixmni
rm p_bin.mgz

They are not Bonferroni-corrected for 2 hemispheres
(--2spaces).

Regarding your design and contrast:

Design has to be matrix of values. You can use qdec to produce
Xg.dat file
with design matrix, then rename it to Xg.csv to be correctly
readable by
PALM.

Regards,

Antonin





Hi Antonin,

As you suggested in discussion forum, I tried to run following
command
after mri_glmfit:

palm -s fsaverage/surf/lh.white -n 10000 -m mask.mgh -Cstat
extent -C
1.974975 -pmethodp none -pmethodr none -twotail -d
Design_MEQ.txt
-t
Contrast_MEQ.txt

Running PALM alpha104 using MATLAB 9.0.0.341360 (R2016a) with
the
following
options:

-s fsaverage/surf/lh.white

-n 10000

-m mask.mgh

-Cstat extent

-C 1.974975

-pmethodp none

-pmethodr none

-twotail

-d Design.txt

-t Contrast.txt

Found FSL in /usr/share/fsl/5.0

Found FreeSurfer in /usr/local/freesurfer

Found SPM in /usr/local/spm12

Error using palm_takeargs (line 1141)

Missing input data (missing "-i").

Error in palm_core (line 33)

[opts,plm] = palm_takeargs(varargin{:});

Error in palm (line 81)

palm_core(varargin{:});

Looks like error is because its missing -i input here, I am not
sure what's
input file here?

Also, I am trying to correlate LGI versus behavioral score,
regressing out
the effect of sex and age. So I just wanted to confirm if my
design.txt and
contrast.txt files are correct here. Please find both
following:

Design file (Variables Behav, Age) as following:

S001 Male 60 36

S003 Female 73 29

S004 Male 48 39

.......so on......

Contrast file as following:
0 0 0.5 0.5 0 0 (same as *.mtx file used for glm_fit)

Thank you so much for your help and time.

On Tue, Mar 7, 2017 at 10:49 AM, Martin Juneja <
mj70...@gmail.com>
wrote:

Hi Antonin,

Thanks a lot for your reply.

Somehow, in the link you sent, I could not find any response
to
your
email. But I can see your email to Anderson and command line
parameters.

As I am not an expert in using FreeSurfer, so would it be
possible for you
to share detailed step-by-step guide and PALM command after I
run
mri_glmfit
command and how and where to include '?h.white.avg.area.mgh'
file?

I would really appreciate any help.

On Mon, Mar 6, 2017 at 4:28 PM, Antonin Skoch <a...@ikem.cz>
wrote:

Dear Martin,

I think yes, you can use PALM with FreeSurfer surfaces, see
my
conversation with Anderson on FSL list:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1604&L=FSL



&D=0&1=FSL&9=A&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=239088


but beware not to forget to include average the vertex area
(?h.white.avg.area.mgh) file.

Antonin


If you don't have an orthogonal design, then you can't use
mri_glmfit-sim. I think you can use PALM:

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM

I have not tried it yet.

Anderson, can you use PALM with surfaces?






On 03/06/2017 05:23 PM, Martin Juneja wrote:
Hi Dr. Greve,

I tried to run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir
--sim perm
1000 3 permcsd --sim-sign abs --cwpvalthresh .05
It gives error that ERROR: design matrix is not
orthogonal,
cannot be
used with permutation.

But when I run: mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir
--sim perm
1000 3 permcsd --sim-sign abs --cwpvalthresh .05
--perm-force, it
works.

I am not sure whether I will have to make the design
matrix
orthogonal. If so, could you please tell me how that can
be
done?

Or using --perm-force should be fine?

Thanks.

On Mon, Mar 6, 2017 at 1:58 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.
edu
<gr...@nmr.mgh.harvard.edu>
<gr...@nmr.mgh.harvard.edu>
<gr...@nmr.mgh.harvard.edu>
<gr...@nmr.mgh.harvard.edu>>> wrote:

   This is a problem with using LGI in that it is already
extremely
   smooth
   that the smoothness exceeds the limit of the look up
table that we
   supply. I  recommend that you not use a gaussian-based
correction
for
   LGI. Instead, use permutation (see mri_glmfit-sim
--help).



   On 03/06/2017 01:36 PM, Martin Juneja wrote:
Hello everyone,

I am trying to extract clusters showing significant
correlation
between LGI and a behavioral measure. I am able to
extract PCC
and
sig.mgh but at the last step when I try to run
simulation command
to
view corrected results and I run:

mri_glmfit-sim --glmdir lh.MEQ_LGI.glmdir --cache 4
neg --cwp
0.05
--2spaces

I get following error:

ERROR: cannot find


/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/
cortex/fwhm35/neg/th40/mc-z.csd

But I can see mc-z.csd file in fwhm30 etc.

Full message on terminal window is attached
following.

Any help would be really appreciated.

----- Full message ----

cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd
MEQ.fsgd
   dods --C
Corr-MEQ-cor.mtx --surf fsaverage lh --cortex
--glmdir
   lh.MEQ_LGI.glmdir

WARNING: unrecognized mri_glmfit cmd option
mri_glmfit.bin

SURFACE: fsaverage lh

log file is lh.MEQ_LGI.glmdir/cache.mri_glmfit-sim.log



/usr/local/freesurfer/bin/mri_glmfit-sim

--glmdir lh.MEQ_LGI.glmdir --cache 4 neg --cwp 0.05
--2spaces

$Id: mri_glmfit-sim,v 1.60 2016/04/30 15:13:36 greve
Exp $

Mon Mar  6 11:11:13 MST 2017

setenv SUBJECTS_DIR
/data/emot/Freesurfer/FreeSurferSegmentation/SB_AgingAll



FREESURFER_HOME /usr/local/freesurfer

Original mri_glmfit command line:

cmdline mri_glmfit.bin --y lh.MEQ_LGI.10.mgh --fsgd
MEQ.fsgd
   dods --C
Corr-MEQ-cor.mtx --surf fsaverage lh --cortex
--glmdir
   lh.MEQ_LGI.glmdir

DoSim = 0

UseCache = 1

DoPoll = 0

DoPBSubmit = 0

DoBackground = 0

DiagCluster = 0

gd2mtx = dods

fwhm = 35.073391

ERROR: cannot find


/usr/local/freesurfer/average/mult-comp-cor/fsaverage/lh/
cortex/fwhm35/neg/th40/mc-z.csd





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Message: 5
Date: Thu, 9 Mar 2017 01:15:26 +0000
From: Elodie Boudes <elodie.boudes@ucalgary.ca>
Subject: [Freesurfer] Issue with mri_segstats to extract cortical
thickness from a volume ROI
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <2B77FD35-72A8-4A94-BDA9-B6A62DC5E316@ucalgary.ca>
Content-Type: text/plain; charset="utf-8"

Hello FreeSurfer community,

I am trying to extract the cortical thickness from a specific ROI.
I followed the pipeline: cortical thickness of a volume-defined ROI. But for the last step:

mri_segstats \
 --seg $SUBJECTS_DIR/fsaverage/surf/lh.fsaverage.ROI5.mgh \
 --in lh.thickness.fsaverage.mgh \
 --sum segstats-ROI5.txt

I encountered an error:
ERROR: dimension inconsistency in source data
Number of surface vertices = 126983
      Number of value vertices = 163842

I tried as suggested in the forum the reshape-factor option as well as the noreshape option for mri_vol2surf and mri_surf2surf. With no success, I obtained a similar error.

The ROI is extracted from another acquisition and is registered to the T1. The T1 has been processed by following the classic pipeline using recon-all ? -all

Any suggestions on how to fix that error or another pipeline that will allow me to get the cortical thickness from inside my ROI?

Thank you


Elodie Boudes
University of Calgary




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Message: 6
Date: Thu, 9 Mar 2017 01:26:46 +0000
From: "Burks, Joshua D (HSC)" <Joshua-Burks@ouhsc.edu>
Subject: [Freesurfer] mri_label2vol error: could not scan # of lines
from label file
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <685F1E2D-5597-4F0B-BEEB-2CB32FFD8812@ouhsc.edu>
Content-Type: text/plain; charset="utf-8"

Hello FreeSurfer Developers,

I?m attempting to convert a dlabel file from the Human Connectome Project to a volumetric ROI that I can use for fiber tractography on other platforms. I followed the tutorial provided by HCP (hcp-users FAQ #9: How do I map data between FreeSurfer ... - HCP Wiki<https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwj3kK2snsjSAhVCMSYKHRJfBFAQFggcMAA&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP.pdf%3Fversion%3D1%26modificationDate%3D1472225460934%26api%3Dv2&usg=AFQjCNF5wUtMevIQ5umsnqe87RzJN9ndXw&sig2=DtNFEuTCbps9LemwkJRseg>) for resampling HCP-derived data for use in FreeSurfer.

When I run the mri_label2vol command:

mri_label2vol: could not scan # of lines from label file
ERROR reading /home/neuroresearch/workbench/test1.label.gii

Does anyone have thoughts on how to troubleshoot this? I have not seen any similar errors described in the list.

1) FreeSurfer version: freesurfer-x86_64-apple-darwin16.4.0-dev-20170302
2) Platform: MacOS 10.12.3
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Message: 7
Date: Thu, 9 Mar 2017 02:17:13 +0000
From: "Peled, Noam" <NPELED@mgh.harvard.edu>
Subject: Re: [Freesurfer] Yet another freeview coordinates question
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<F77601247B59244F9311E7776B9DAE9618464DB0@PHSX10MB10.partners.org>
Content-Type: text/plain; charset="windows-1256"

ok, I've figured out that this is indeed the case:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg23348.html

Also, following these instructions I was able to get RAS from the tkreg RAS in FreeView:
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024293.html

Thanks,
Noam
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Peled, Noam [NPELED@mgh.harvard.edu]
Sent: Wednesday, March 08, 2017 9:27 AM
To: Freesurfer support list ?[freesurfer@nmr.mgh.harvard.edu]?
Subject: [Freesurfer] Yet another freeview coordinates question

Hey all,
When loading two T1 in freeview, one for a subject and one for fsaverage, and switching between them, only the tkreg RAS coordinates changes while moving the mouse, not the RAS.
Does it mean that the RAS in freeview is always in MNI305?

Thanks,
Noam
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Message: 8
Date: Wed, 8 Mar 2017 21:27:02 -0500
From: "Dorian P." <alb.net@gmail.com>
Subject: [Freesurfer] Results from R to Freesurfer
To: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAF9pfmZN7VXYjotbDzoxFihwNXq7gKDp3eVr4gx9QMPZVcbY+w@mail.gmail.com>
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Hi Freesurfers,

I am using R to perform thickness analyses. All subjects are transformed in
fsaverage space and all values are placed in a matrix with 327684 columns
(163842 for each hemisphere). I put the results back in a surface file
(.asc format) and then convert it to a binary Freesurfer format. I then
open the files in Freesurfer to view them.

Overall the results make sense and fall in the right places. But I am
concerned that some results fall into the corpus callosum, which, if I
remember correctly should not have any thickness value, and therefore no
results.

Here is a screenshot:
[image: Inline image 1]

Can someone help my understand what might be wrong? Or, if this is normal,
why I am finding thickness results where there is no thickness?

Is there a way to find label numbers for each vertex in fsaverage space
(i.e. list of parcel number for each vertex). This might be useful to
exclude certain vertices or compute summery statistics of the results
directly in R.

Third question, is it possible to threshold the above map based on minimal
cluster area (i.e., in mri_surfcluster). If yes, do I need to prepare a
binary file with p-values for thresholding (0-1), or can I use
mri_surfcluster with t-score maps (0-Inf)?

Thank you for your help.
Dorian
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