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.edumailto:freesurfer-request@nmr.mgh.harvard.edu wrote:

Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu

You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."

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 ? ? > ? ? >

-------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/b6...

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

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

-------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/13...

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

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

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/d1...

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

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

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

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

-------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/07...

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

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

-------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170309/1c...

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

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 Wikihttps://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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170309/15...

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

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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170309/c4...

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

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 Content-Type: text/plain; charset="utf-8"

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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/e4... -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 390528 bytes Desc: not available Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170308/e4...

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

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

End of Freesurfer Digest, Vol 157, Issue 26 *******************************************