Dear Sahil,
I would suggest at first to make check of your GLM PALM setup by comparing mri_glmfit and PALM output files (using the same design and contrast):
1. values of gamma.mgh should correspond to values of *cope.mgh
2. values of F.mgh should be (*dpv_tstat.mgh) ^2.
3. values of sig.mgh should be {roughly) values of -log10(*dpv_tstat_uncp.mgh) - I am currently not sure why I do not get exact correspondence here.
4. When you threshold the sig.mgh by some threshold in freeview (let it be x) and use the same corresponding cluster-forming z-score threshold -C in PALM computed as qnorm(1-10^-x/2) (and use two-sided hypothesis by specifying -twotail), your *clustere_tstat.mgz should show the clusters with the same shape (regardless of their values, the clusters will be defined by non-zero value, other vertices would be zero) as the thresholded display of sig.mgh (computed by -two sided hypothesis).
If there is any inconsistence, then there is probably something wrong with your PALM setup.
Antonin
Dear Antonin,
Could you please have a look at the attached screen shot. This map is with full number of permutations, without -approx tail -n 500 -nouncorrected
Here, I noticed that its only *_dpv_tstat.mgz which looks correct and giving very high negative value, close to that big cluster, small positive values at red clusters and the value changes when I change the position of cursor.
*_dpv_tstat_fwep shows value of 1 mostly but shows between 0.97 and 1 close/at the red clusters and 1 elsewhere, even at the big blue negative cluster.
Third, *_clustere_tstat_fwep and *_clustere_tstat shows 1 and 0 respectively everywhere, even at the big blue negative cluster.
If there is something fishy with the analysis, would you mind looking at the data and the detailed commands I am using to run the analysis?
Thanks a lot, Sahil
On Wed, Mar 8, 2017 at 11:54 PM, Antonin Skoch ansk@ikem.cz wrote:
Dear Sahil,
to assure that there is no other issue with your setup, I would recommend to obtain cluster-wise p-pvalue of that big cluster to see if it is reasonable, i.e. if it is somewhat close to the significance.
Therefore, I would load *_clustere_tstat_fwep and click to the area of big cluster and see what the values of the vertices in that region are.
Or, I would increase --thmax in mri_surfcluster to see the cluster-wise p-value(s). If you use --thmax 0.9999 (or maybe 1), you should see cluster-wise FWER corrected p-values of all clusters formed by used cluster-forming threshold.
I would also maybe try to switch-off tail approximation and run it in full number of permutations (i.e. do not use -approx tail -n 500 -nouncorrected).
If there is no other issue, then yes, the conclusion would be, that for the used cluster-extent inference and currently set cluster-forming threshold, none of the clusters survived FWER correction at cluster-wise p-value threshold of 0.05.
Antonin
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 a...@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:
freesurfer@nmr.mgh.harvard.edu/msg52042.html" title="http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg52042.html" target="_blank">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 a...@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.br...@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 mj70...@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 < wink...@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 a...@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 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@nmr.mgh.harvard.edu
-
Antonin Skoch