Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas N Greve]

All the values are between 0 and 1, so I suspect this is a map of 
p-values, not a map of -log10(p). Is that right? If so, convert it to 
-log10(p) and rerun. You can do this in matlab with
p = MRIread('rh_time.mgh');
sig = p;
sig.vol = -log10(abs(p.vol));
MRIwrite(sig,'sig.mgh');



On 03/03/2016 12:34 PM, Jennifer Legault wrote:
> Absolutely,  here it is attached.  Thank you for looking into this.
>
> Best,
>
> Jen
>
> On Thu, Mar 3, 2016 at 12:24 PM, Douglas N Greve 
> > wrote:
>
> Can you send me rh_time_spval.mgh?
>
>
>
> On 03/01/2016 04:42 PM, Jennifer Legault wrote:
> > Hi Doug,
> >
> > Thank you for responding.  I actually realized what was the
> matter (I
> > had specified the path for fsaverage which led to the error; this is
> > no longer an issue so long as I use "--subject fsaverage" instead of
> > "--subject /path/fsaverage."
> >
> > Here is the command I've been running for mri_surfcluster:
> >
> > mri_surfcluster --subject fsaverage --hemi rh --in
> > /path/rh_time_spval.mgh --csd
> >
> 
> /usr/global/freesurfer/5.3.0/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm01/pos/th40/mc-z.csd
> > --cwpvalthresh 0.0001 --fdr .05 --no-fixmni --annot aparc --sign pos
> > --o /path/rh_time_cluster_cwp0001.mgh  --cwsig
> > /path/rh_time_cluster_mni_cwp0001.mgh --sum
> > /path/rh_time_cluster_mni_sum
> >
> >
> > I do consistently have an issue though where the final output
> seems to
> > be inaccurate (even with CWP of p<.0001 and FDR correction, I
> receive
> > over 800 significant clusters).  I am assuming this is a problem
> with
> > the LME multivariate analysis script, although I am not exactly sure
> > which part of the script needs to be changed. Attached is a
> > screenshot of the output (visualized with freeview), as well as the
> > matlab script and the qdec file (with fsid, fsid-base, MRI (time),
> > group, and eTIV as columns).  This script is geared towards
> examining
> > changes in the brain after cognitive training lasting 2-3 weeks.  If
> > you have the time to look over this and let me know of any
> > recommendations you have, it would be greatly appreciated.
> >
> > Best,
> >
> > Jennifer Legault
> >
> > On Tue, Mar 1, 2016 at 3:27 PM, Douglas N Greve
> > >
> wrote:
> >> can you send your command line and terminal output?
> >>
> >> On 02/25/2016 01:52 PM, Jennifer Legault wrote:
> >>> Hi Douglas,
> >>>
> >>> Thank you for all your help.  When I say "volume" I do mean the FS
> >>> thickness*area measure.  I ran the mri_glmfit with --osgm and
> for the
> >>> FWHM received the value of .925737. Assuming that this rounds
> up to 1,
> >>> I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to
> >>> find the CSD file and I selected the fwhm01 csd file.
> >>>
> >>> I then ran the mri_surfcluster command, however, I got the
> following
> >>> error:
> >>>
> >>> ERROR: you have specified srcsubjid=fsaverage on cmdline, but
> >>> CSD file was created with fsaverage
> >>>
> >>> Any suggestions you have would be appreciated.
> >>>
> >>> Best,
> >>>
> >>> Jen
> >>>
> >>> On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve
> >>> 
>  >> wrote:
> >>>
> >>>  by "volume" do you mean a VBM-type analysis or do you
> mean the volume
> >>>  that comes out of FS (thickness*area)? If you are going
> to use a
> >>>  clusterwise correction, then you have to have a FWHM
> measurement. You
> >>>  can try analyzing it in mri_glmfit with --osgm just to
> get the
> >>>  FWHM out
> >>>  of it.
> >>>
> >>>  You should be able to output a .mgh file instead of a .w file
> >>>
> >>>
> >>>  On 02/11/2016 01:07 PM, Jennifer Legault wrote:
> >>>  > That's very useful, thank you. In terms of FWHM, I am
> examining
> >>>  gray
> >>>  > matter volume, not cortical thickness, and was
> previously instructed
> >>>  > by Martin Reuter not to smooth these data.  Do you think it
> >>>  would make
> >>>  > sense then to just use the fwhm01?  And in terms of the
> voxel-wise
> >>>  > threshold, is there a commonly used value for GM volume
> data?  I am
> >>>  > still new to freesurfer and I appreciate any feedback.
> >>>  >
> >>>  > For visualization, after I run the mri_surfcluster the
> only outputs
> >>>  > are a summary file and a .w file, and freeview doesn't
> 

Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas N Greve]

Can you send me rh_time_spval.mgh?



On 03/01/2016 04:42 PM, Jennifer Legault wrote:
> Hi Doug,
>
> Thank you for responding.  I actually realized what was the matter (I
> had specified the path for fsaverage which led to the error; this is
> no longer an issue so long as I use "--subject fsaverage" instead of
> "--subject /path/fsaverage."
>
> Here is the command I've been running for mri_surfcluster:
>
> mri_surfcluster --subject fsaverage --hemi rh --in
> /path/rh_time_spval.mgh --csd
> /usr/global/freesurfer/5.3.0/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm01/pos/th40/mc-z.csd
> --cwpvalthresh 0.0001 --fdr .05 --no-fixmni --annot aparc --sign pos
> --o /path/rh_time_cluster_cwp0001.mgh  --cwsig
> /path/rh_time_cluster_mni_cwp0001.mgh --sum
> /path/rh_time_cluster_mni_sum
>
>
> I do consistently have an issue though where the final output seems to
> be inaccurate (even with CWP of p<.0001 and FDR correction, I receive
> over 800 significant clusters).  I am assuming this is a problem with
> the LME multivariate analysis script, although I am not exactly sure
> which part of the script needs to be changed.  Attached is a
> screenshot of the output (visualized with freeview), as well as the
> matlab script and the qdec file (with fsid, fsid-base, MRI (time),
> group, and eTIV as columns).  This script is geared towards examining
> changes in the brain after cognitive training lasting 2-3 weeks.  If
> you have the time to look over this and let me know of any
> recommendations you have, it would be greatly appreciated.
>
> Best,
>
> Jennifer Legault
>
> On Tue, Mar 1, 2016 at 3:27 PM, Douglas N Greve
>  wrote:
>> can you send your command line and terminal output?
>>
>> On 02/25/2016 01:52 PM, Jennifer Legault wrote:
>>> Hi Douglas,
>>>
>>> Thank you for all your help.  When I say "volume" I do mean the FS
>>> thickness*area measure.  I ran the mri_glmfit with --osgm and for the
>>> FWHM received the value of .925737. Assuming that this rounds up to 1,
>>> I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to
>>> find the CSD file and I selected the fwhm01 csd file.
>>>
>>> I then ran the mri_surfcluster command, however, I got the following
>>> error:
>>>
>>> ERROR: you have specified srcsubjid=fsaverage on cmdline, but
>>> CSD file was created with fsaverage
>>>
>>> Any suggestions you have would be appreciated.
>>>
>>> Best,
>>>
>>> Jen
>>>
>>> On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve
>>> > wrote:
>>>
>>>  by "volume" do you mean a VBM-type analysis or do you mean the volume
>>>  that comes out of FS (thickness*area)? If you are going to use a
>>>  clusterwise correction, then you have to have a FWHM measurement. You
>>>  can try analyzing it in mri_glmfit with --osgm just to get the
>>>  FWHM out
>>>  of it.
>>>
>>>  You should be able to output a .mgh file instead of a .w file
>>>
>>>
>>>  On 02/11/2016 01:07 PM, Jennifer Legault wrote:
>>>  > That's very useful, thank you.  In terms of FWHM, I am examining
>>>  gray
>>>  > matter volume, not cortical thickness, and was previously instructed
>>>  > by Martin Reuter not to smooth these data.  Do you think it
>>>  would make
>>>  > sense then to just use the fwhm01?  And in terms of the voxel-wise
>>>  > threshold, is there a commonly used value for GM volume data?  I am
>>>  > still new to freesurfer and I appreciate any feedback.
>>>  >
>>>  > For visualization, after I run the mri_surfcluster the only outputs
>>>  > are a summary file and a .w file, and freeview doesn't accept this
>>>  > format.  Is it possible to have a cluster-wise corrected map (a
>>>  > sig.cluster.mgh file) as they do for the Clusterwise Correction for
>>>  > Multiple Comparisons tutorial here
>>>  >
>>>  ?
>>>  >
>>>  >
>>>  > Best,
>>>  >
>>>  > Jen
>>>  >
>>>  > On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve
>>>  > 
>>>  >>  >> wrote:
>>>  >
>>>  >
>>>  >
>>>  > On 02/11/2016 11:19 AM, Jennifer Legault wrote:
>>>  > > Thank you for your response.  Do I need to run the glm_fit-sim
>>>  > command
>>>  > > to make the csd file?  I feel this would be inappropriate
>>>  for my
>>>  > data
>>>  > > since I already ran the LME model.
>>>  > No, look in
>>>  $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will
>>>  > need the FWHM though
>>>  > >
>>>  > > Second, is there an argument to make an output file that
>>>  can be
>>>  > > visualized via freeview?  In other words, how can I view
>>>  my cluster
>>>

Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas N Greve]

can you send your command line and terminal output?

On 02/25/2016 01:52 PM, Jennifer Legault wrote:
> Hi Douglas,
>
> Thank you for all your help.  When I say "volume" I do mean the FS 
> thickness*area measure.  I ran the mri_glmfit with --osgm and for the 
> FWHM received the value of .925737. Assuming that this rounds up to 1, 
> I then went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to 
> find the CSD file and I selected the fwhm01 csd file.
>
> I then ran the mri_surfcluster command, however, I got the following 
> error:
>
> ERROR: you have specified srcsubjid=fsaverage on cmdline, but
> CSD file was created with fsaverage
>
> Any suggestions you have would be appreciated.
>
> Best,
>
> Jen
>
> On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve 
> > wrote:
>
> by "volume" do you mean a VBM-type analysis or do you mean the volume
> that comes out of FS (thickness*area)? If you are going to use a
> clusterwise correction, then you have to have a FWHM measurement. You
> can try analyzing it in mri_glmfit with --osgm just to get the
> FWHM out
> of it.
>
> You should be able to output a .mgh file instead of a .w file
>
>
> On 02/11/2016 01:07 PM, Jennifer Legault wrote:
> > That's very useful, thank you.  In terms of FWHM, I am examining
> gray
> > matter volume, not cortical thickness, and was previously instructed
> > by Martin Reuter not to smooth these data.  Do you think it
> would make
> > sense then to just use the fwhm01?  And in terms of the voxel-wise
> > threshold, is there a commonly used value for GM volume data?  I am
> > still new to freesurfer and I appreciate any feedback.
> >
> > For visualization, after I run the mri_surfcluster the only outputs
> > are a summary file and a .w file, and freeview doesn't accept this
> > format.  Is it possible to have a cluster-wise corrected map (a
> > sig.cluster.mgh file) as they do for the Clusterwise Correction for
> > Multiple Comparisons tutorial here
> >
> ?
> >
> >
> > Best,
> >
> > Jen
> >
> > On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve
> > 
>  >> wrote:
> >
> >
> >
> > On 02/11/2016 11:19 AM, Jennifer Legault wrote:
> > > Thank you for your response.  Do I need to run the glm_fit-sim
> > command
> > > to make the csd file?  I feel this would be inappropriate
> for my
> > data
> > > since I already ran the LME model.
> > No, look in
> $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will
> > need the FWHM though
> > >
> > > Second, is there an argument to make an output file that
> can be
> > > visualized via freeview?  In other words, how can I view
> my cluster
> > > thresholded data?
> > You can use freeview, something like
> > freeview -f lh.inflated:overlay=sig.mgh
> > There are other options for loading annotations and
> curvature. See the
> > freeview help
> > >
> > > Your help is greatly appreciated,
> > >
> > > Jen
> > >
> > >
> > >
> > > On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve
> > >  
> >
> > 
> >   > >
> > > There is a (very long) command line on that page. Mainly you
> > need
> > > a csd file. To get that you need the FWHM of your
> analysis, the
> > > voxel-wise threshold, and the sign of the contrast (or
> abs).
> > Then
> > > the relevant output will be the --sum. You can run it with
> > --help
> > > to get more info.
> > >
> > >
> > > On 2/10/16 5:11 PM, Jennifer Legault wrote:
> > >> Thank you very much for your help! I still received a
> "cannot
> > >> read file type" error when I only added the path to
> the output
> > >> --o part, however when I also added the path to the
> input file,
> > >> it worked!
> > >>
> > >> I do have one more question: Which argument can I add so
> > that in
> > >> my output file I see the clusterwise P value, like it
> is shown
> > >> here
> > >>
> > 
> 
> 

Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Jennifer Legault]

Hi Douglas,

Thank you for all your help.  When I say "volume" I do mean the FS
thickness*area measure.  I ran the mri_glmfit with --osgm and for the FWHM
received the value of .925737.  Assuming that this rounds up to 1, I then
went to $FREESURFER_HOME/average/mult-comp-cor/fsaverage to find the CSD
file and I selected the fwhm01 csd file.

I then ran the mri_surfcluster command, however, I got the following error:

ERROR: you have specified srcsubjid=fsaverage on cmdline, but
CSD file was created with fsaverage

Any suggestions you have would be appreciated.

Best,

Jen

On Thu, Feb 11, 2016 at 1:32 PM, Douglas N Greve 
wrote:

> by "volume" do you mean a VBM-type analysis or do you mean the volume
> that comes out of FS (thickness*area)? If you are going to use a
> clusterwise correction, then you have to have a FWHM measurement. You
> can try analyzing it in mri_glmfit with --osgm just to get the FWHM out
> of it.
>
> You should be able to output a .mgh file instead of a .w file
>
>
> On 02/11/2016 01:07 PM, Jennifer Legault wrote:
> > That's very useful, thank you.  In terms of FWHM, I am examining gray
> > matter volume, not cortical thickness, and was previously instructed
> > by Martin Reuter not to smooth these data.  Do you think it would make
> > sense then to just use the fwhm01?  And in terms of the voxel-wise
> > threshold, is there a commonly used value for GM volume data?  I am
> > still new to freesurfer and I appreciate any feedback.
> >
> > For visualization, after I run the mri_surfcluster the only outputs
> > are a summary file and a .w file, and freeview doesn't accept this
> > format.  Is it possible to have a cluster-wise corrected map (a
> > sig.cluster.mgh file) as they do for the Clusterwise Correction for
> > Multiple Comparisons tutorial here
> > ?
> >
> >
> > Best,
> >
> > Jen
> >
> > On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve
> > > wrote:
> >
> >
> >
> > On 02/11/2016 11:19 AM, Jennifer Legault wrote:
> > > Thank you for your response.  Do I need to run the glm_fit-sim
> > command
> > > to make the csd file?  I feel this would be inappropriate for my
> > data
> > > since I already ran the LME model.
> > No, look in $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You
> will
> > need the FWHM though
> > >
> > > Second, is there an argument to make an output file that can be
> > > visualized via freeview?  In other words, how can I view my cluster
> > > thresholded data?
> > You can use freeview, something like
> > freeview -f lh.inflated:overlay=sig.mgh
> > There are other options for loading annotations and curvature. See
> the
> > freeview help
> > >
> > > Your help is greatly appreciated,
> > >
> > > Jen
> > >
> > >
> > >
> > > On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve
> > > 
> >  > >> wrote:
> > >
> > > There is a (very long) command line on that page. Mainly you
> > need
> > > a csd file. To get that you need the FWHM of your analysis, the
> > > voxel-wise threshold, and the sign of the contrast (or abs).
> > Then
> > > the relevant output will be the --sum. You can run it with
> > --help
> > > to get more info.
> > >
> > >
> > > On 2/10/16 5:11 PM, Jennifer Legault wrote:
> > >> Thank you very much for your help!  I still received a "cannot
> > >> read file type" error when I only added the path to the output
> > >> --o part, however when I also added the path to the input
> file,
> > >> it worked!
> > >>
> > >> I do have one more question: Which argument can I add so
> > that in
> > >> my output file I see the clusterwise P value, like it is shown
> > >> here
> > >>
> >  <
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary
> >?
> > >>
> > >> Best,
> > >>
> > >> Jen
> > >>
> > >> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve
> > >> 
> >  > >> wrote:
> > >>
> > >> I meant for the output files, so the --o in particular
> > >>
> > >> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
> > >> > Douglas,
> > >> >
> > >> > Thank you for your quick response. When I add --sd
> > >> [path_location], I
> > >> > get the following error:
> > >> > Loading source values
> > >> > mri_read(): couldn't determine type of 

Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Jennifer Legault]

Thank you for your response.  Do I need to run the glm_fit-sim command to
make the csd file?  I feel this would be inappropriate for my data since I
already ran the LME model.

Second, is there an argument to make an output file that can be visualized
via freeview?  In other words, how can I view my cluster thresholded data?

Your help is greatly appreciated,

Jen



On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve 
wrote:

> There is a (very long) command line on that page. Mainly you need a csd
> file. To get that you need the FWHM of your analysis, the voxel-wise
> threshold, and the sign of the contrast (or abs). Then the relevant output
> will be the --sum. You can run it with --help to get more info.
>
>
> On 2/10/16 5:11 PM, Jennifer Legault wrote:
>
> Thank you very much for your help!  I still received a "cannot read file
> type" error when I only added the path to the output --o part, however when
> I also added the path to the input file, it worked!
>
> I do have one more question: Which argument can I add so that in my output
> file I see the clusterwise P value, like it is shown here
> 
> ?
>
> Best,
>
> Jen
>
> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>> I meant for the output files, so the --o in particular
>>
>> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
>> > Douglas,
>> >
>> > Thank you for your quick response.  When I add --sd [path_location], I
>> > get the following error:
>> > Loading source values
>> > mri_read(): couldn't determine type of file
>> [path_location]/rh_time_spval
>> > ERROR: could not read rh_time_spval as type
>> >
>> > Should I use another argument?
>> >
>> > Best,
>> >
>> > Jen
>> >
>> >
>> >
>> > On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve
>> > > wrote:
>> >
>> > Try specifying the full path to the output
>> >
>> > On 02/10/2016 12:59 PM, Jennifer Legault wrote:
>> > > Dear experts,
>> > >
>> > > I am trying to use the cluster thresholding command for my
>> > freesurfer
>> > > LME outputs as referred to here
>> > >
>> > > >.
>> > > Any feedback or comments would be greatly appreciated.
>> > >
>> > > I am aware that there have been permission denied errors when
>> using
>> > > mri_surfcluster and that applying this patch
>> > >
>> > <
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg
>> >
>> > > should solve the problem (which I tried), however I am still
>> either
>> > > receiving errors stating the permission is denied.
>> > >
>> > > This is the command I am trying to run:
>> > >
>> > >  mri_surfcluster --subject fsaverage --hemi rh --in
>> > rh_time_spval.mgh
>> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster
>> --sum
>> > > rh_time_cluster_sum
>> > >
>> > >
>> > > Here is the error log:
>> > >
>> > > mri_surfcluster --subject fsaverage --hemi rh --in
>> rh_time_spval.mgh
>> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster
>> --sum
>> > > rh_time_cluster_sum thsign = pos, id = 1
>> > > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05
>> > greve Exp $
>> > > hemi   = rh
>> > > srcid  = rh_time_spval.mgh
>> > > srcsubjid  = fsaverage
>> > > srcsurf= white
>> > > srcframe   = 0
>> > > thsign = pos
>> > > thmin  = -1
>> > > thmax  = -1
>> > > fdr= 0.05
>> > > minarea= 0
>> > > xfmfile= talairach.xfm
>> > > nth = -1
>> > > outid= rh_time_cluster paint
>> > > sumfile  = rh_time_cluster_sum
>> > > subjectsdir= /gpfs/home/jtl190/work/structurals
>> > > FixMNI = 1
>> > > - XFM matrix (RAS2RAS) ---
>> > >
>> >
>>  /gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm
>> > >  1.000   0.000   0.000   0.000;
>> > >  0.000   1.000   0.000   0.000;
>> > >  0.000   0.000   1.000   0.000;
>> > >  0.000   0.000   0.000   1.000;
>> > > 
>> > > Reading source surface
>> > > /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white
>> > > Done reading source surface
>> > > Computing metric properties
>> > > Loading source values
>> > > number of voxels in search space = 163842
>> > > Done loading source values (nvtxs = 163842)
>> > > overall max = 1 at vertex 27
>> > > overall min = 1.52021e-05 at vertex 125620
>> > > surface nvertices 163842
>> > > surface area 65020.929688
>> > > surface area 65020.765625
>> > > Setting voxel-wise threshold with FDR = 

Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas N Greve]

On 02/11/2016 11:19 AM, Jennifer Legault wrote:
> Thank you for your response.  Do I need to run the glm_fit-sim command 
> to make the csd file?  I feel this would be inappropriate for my data 
> since I already ran the LME model.
No, look in  $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will 
need the FWHM though
>
> Second, is there an argument to make an output file that can be 
> visualized via freeview?  In other words, how can I view my cluster 
> thresholded data?
You can use freeview, something like
freeview -f lh.inflated:overlay=sig.mgh
There are other options for loading annotations and curvature. See the 
freeview help
>
> Your help is greatly appreciated,
>
> Jen
>
>
>
> On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve 
> > wrote:
>
> There is a (very long) command line on that page. Mainly you need
> a csd file. To get that you need the FWHM of your analysis, the
> voxel-wise threshold, and the sign of the contrast (or abs). Then
> the relevant output will be the --sum. You can run it with --help
> to get more info.
>
>
> On 2/10/16 5:11 PM, Jennifer Legault wrote:
>> Thank you very much for your help!  I still received a "cannot
>> read file type" error when I only added the path to the output
>> --o part, however when I also added the path to the input file,
>> it worked!
>>
>> I do have one more question: Which argument can I add so that in
>> my output file I see the clusterwise P value, like it is shown
>> here
>> 
>> ?
>>
>> Best,
>>
>> Jen
>>
>> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve
>> > wrote:
>>
>> I meant for the output files, so the --o in particular
>>
>> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
>> > Douglas,
>> >
>> > Thank you for your quick response. When I add --sd
>> [path_location], I
>> > get the following error:
>> > Loading source values
>> > mri_read(): couldn't determine type of file
>> [path_location]/rh_time_spval
>> > ERROR: could not read rh_time_spval as type
>> >
>> > Should I use another argument?
>> >
>> > Best,
>> >
>> > Jen
>> >
>> >
>> >
>> > On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve
>> > > 
>> > >> wrote:
>> >
>> > Try specifying the full path to the output
>> >
>> > On 02/10/2016 12:59 PM, Jennifer Legault wrote:
>> > > Dear experts,
>> > >
>> > > I am trying to use the cluster thresholding command
>> for my
>> > freesurfer
>> > > LME outputs as referred to here
>> > >
>> >   
>>  
>> .
>> > > Any feedback or comments would be greatly appreciated.
>> > >
>> > > I am aware that there have been permission denied
>> errors when using
>> > > mri_surfcluster and that applying this patch
>> > >
>> >   
>>  
>> 
>> > > should solve the problem (which I tried), however I
>> am still either
>> > > receiving errors stating the permission is denied.
>> > >
>> > > This is the command I am trying to run:
>> > >
>> > >  mri_surfcluster --subject fsaverage --hemi rh --in
>> > rh_time_spval.mgh
>> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o
>> rh_time_cluster  --sum
>> > > rh_time_cluster_sum
>> > >
>> > >
>> > > Here is the error log:
>> > >
>> > > mri_surfcluster --subject fsaverage --hemi rh --in
>> rh_time_spval.mgh
>> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o
>> rh_time_cluster  --sum
>> > > rh_time_cluster_sum  thsign = pos, id = 1
>> > > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31
>> 22:10:05
>> > greve Exp $
>> > > hemi   = rh
>> > > srcid  = rh_time_spval.mgh
>> > > srcsubjid  = fsaverage
>> > > srcsurf= white
>> > > srcframe   = 0
>> > > thsign = pos
>> > > thmin  = -1
>> > > thmax  = -1
>> > > fdr= 0.05
>> > > minarea 

Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Jennifer Legault]

That's very useful, thank you.  In terms of FWHM, I am examining gray
matter volume, not cortical thickness, and was previously instructed by
Martin Reuter not to smooth these data.  Do you think it would make sense
then to just use the fwhm01?  And in terms of the voxel-wise threshold, is
there a commonly used value for GM volume data?  I am still new to
freesurfer and I appreciate any feedback.

For visualization, after I run the mri_surfcluster the only outputs are a
summary file and a .w file, and freeview doesn't accept this format.  Is it
possible to have a cluster-wise corrected map (a sig.cluster.mgh file) as
they do for the Clusterwise Correction for Multiple Comparisons tutorial
here ?


Best,

Jen

On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve  wrote:

>
>
> On 02/11/2016 11:19 AM, Jennifer Legault wrote:
> > Thank you for your response.  Do I need to run the glm_fit-sim command
> > to make the csd file?  I feel this would be inappropriate for my data
> > since I already ran the LME model.
> No, look in  $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will
> need the FWHM though
> >
> > Second, is there an argument to make an output file that can be
> > visualized via freeview?  In other words, how can I view my cluster
> > thresholded data?
> You can use freeview, something like
> freeview -f lh.inflated:overlay=sig.mgh
> There are other options for loading annotations and curvature. See the
> freeview help
> >
> > Your help is greatly appreciated,
> >
> > Jen
> >
> >
> >
> > On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve
> > > wrote:
> >
> > There is a (very long) command line on that page. Mainly you need
> > a csd file. To get that you need the FWHM of your analysis, the
> > voxel-wise threshold, and the sign of the contrast (or abs). Then
> > the relevant output will be the --sum. You can run it with --help
> > to get more info.
> >
> >
> > On 2/10/16 5:11 PM, Jennifer Legault wrote:
> >> Thank you very much for your help!  I still received a "cannot
> >> read file type" error when I only added the path to the output
> >> --o part, however when I also added the path to the input file,
> >> it worked!
> >>
> >> I do have one more question: Which argument can I add so that in
> >> my output file I see the clusterwise P value, like it is shown
> >> here
> >> <
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSummary
> >?
> >>
> >> Best,
> >>
> >> Jen
> >>
> >> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve
> >> >
> wrote:
> >>
> >> I meant for the output files, so the --o in particular
> >>
> >> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
> >> > Douglas,
> >> >
> >> > Thank you for your quick response. When I add --sd
> >> [path_location], I
> >> > get the following error:
> >> > Loading source values
> >> > mri_read(): couldn't determine type of file
> >> [path_location]/rh_time_spval
> >> > ERROR: could not read rh_time_spval as type
> >> >
> >> > Should I use another argument?
> >> >
> >> > Best,
> >> >
> >> > Jen
> >> >
> >> >
> >> >
> >> > On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve
> >> >  >> 
> >>  >> >> wrote:
> >> >
> >> > Try specifying the full path to the output
> >> >
> >> > On 02/10/2016 12:59 PM, Jennifer Legault wrote:
> >> > > Dear experts,
> >> > >
> >> > > I am trying to use the cluster thresholding command
> >> for my
> >> > freesurfer
> >> > > LME outputs as referred to here
> >> > >
> >> >
> >>  <
> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels>.
> >> > > Any feedback or comments would be greatly appreciated.
> >> > >
> >> > > I am aware that there have been permission denied
> >> errors when using
> >> > > mri_surfcluster and that applying this patch
> >> > >
> >> >
> >>  <
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg
> >
> >> > > should solve the problem (which I tried), however I
> >> am still either
> >> > > receiving errors stating the permission is denied.
> >> > >
> >> > > This is the command I am trying to run:
> >> > >
> >> > >  mri_surfcluster --subject 

Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas N Greve]

by "volume" do you mean a VBM-type analysis or do you mean the volume 
that comes out of FS (thickness*area)? If you are going to use a 
clusterwise correction, then you have to have a FWHM measurement. You 
can try analyzing it in mri_glmfit with --osgm just to get the FWHM out 
of it.

You should be able to output a .mgh file instead of a .w file


On 02/11/2016 01:07 PM, Jennifer Legault wrote:
> That's very useful, thank you.  In terms of FWHM, I am examining gray 
> matter volume, not cortical thickness, and was previously instructed 
> by Martin Reuter not to smooth these data.  Do you think it would make 
> sense then to just use the fwhm01?  And in terms of the voxel-wise 
> threshold, is there a commonly used value for GM volume data?  I am 
> still new to freesurfer and I appreciate any feedback.
>
> For visualization, after I run the mri_surfcluster the only outputs 
> are a summary file and a .w file, and freeview doesn't accept this 
> format.  Is it possible to have a cluster-wise corrected map (a 
> sig.cluster.mgh file) as they do for the Clusterwise Correction for 
> Multiple Comparisons tutorial here 
> ?
>
>
> Best,
>
> Jen
>
> On Thu, Feb 11, 2016 at 11:39 AM, Douglas N Greve 
> > wrote:
>
>
>
> On 02/11/2016 11:19 AM, Jennifer Legault wrote:
> > Thank you for your response.  Do I need to run the glm_fit-sim
> command
> > to make the csd file?  I feel this would be inappropriate for my
> data
> > since I already ran the LME model.
> No, look in $FREESURFER_HOME/average/mult-comp-cor/fsaverage. You will
> need the FWHM though
> >
> > Second, is there an argument to make an output file that can be
> > visualized via freeview?  In other words, how can I view my cluster
> > thresholded data?
> You can use freeview, something like
> freeview -f lh.inflated:overlay=sig.mgh
> There are other options for loading annotations and curvature. See the
> freeview help
> >
> > Your help is greatly appreciated,
> >
> > Jen
> >
> >
> >
> > On Wed, Feb 10, 2016 at 11:04 PM, Douglas Greve
> > 
>  >> wrote:
> >
> > There is a (very long) command line on that page. Mainly you
> need
> > a csd file. To get that you need the FWHM of your analysis, the
> > voxel-wise threshold, and the sign of the contrast (or abs).
> Then
> > the relevant output will be the --sum. You can run it with
> --help
> > to get more info.
> >
> >
> > On 2/10/16 5:11 PM, Jennifer Legault wrote:
> >> Thank you very much for your help!  I still received a "cannot
> >> read file type" error when I only added the path to the output
> >> --o part, however when I also added the path to the input file,
> >> it worked!
> >>
> >> I do have one more question: Which argument can I add so
> that in
> >> my output file I see the clusterwise P value, like it is shown
> >> here
> >>   
>  
> ?
> >>
> >> Best,
> >>
> >> Jen
> >>
> >> On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve
> >> 
>  >> wrote:
> >>
> >> I meant for the output files, so the --o in particular
> >>
> >> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
> >> > Douglas,
> >> >
> >> > Thank you for your quick response. When I add --sd
> >> [path_location], I
> >> > get the following error:
> >> > Loading source values
> >> > mri_read(): couldn't determine type of file
> >> [path_location]/rh_time_spval
> >> > ERROR: could not read rh_time_spval as type
> >> >
> >> > Should I use another argument?
> >> >
> >> > Best,
> >> >
> >> > Jen
> >> >
> >> >
> >> >
> >> > On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve
> >> >  
> >>  >
> >>  
> >>   >> >
> >> > Try specifying the full path to the output
> >>  

Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas N Greve]

I meant for the output files, so the --o in particular

On 02/10/2016 01:47 PM, Jennifer Legault wrote:
> Douglas,
>
> Thank you for your quick response.  When I add --sd [path_location], I 
> get the following error:
> Loading source values
> mri_read(): couldn't determine type of file [path_location]/rh_time_spval
> ERROR: could not read rh_time_spval as type
>
> Should I use another argument?
>
> Best,
>
> Jen
>
>
>
> On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve 
> > wrote:
>
> Try specifying the full path to the output
>
> On 02/10/2016 12:59 PM, Jennifer Legault wrote:
> > Dear experts,
> >
> > I am trying to use the cluster thresholding command for my
> freesurfer
> > LME outputs as referred to here
> >
> .
> > Any feedback or comments would be greatly appreciated.
> >
> > I am aware that there have been permission denied errors when using
> > mri_surfcluster and that applying this patch
> >
> 
> 
> > should solve the problem (which I tried), however I am still either
> > receiving errors stating the permission is denied.
> >
> > This is the command I am trying to run:
> >
> >  mri_surfcluster --subject fsaverage --hemi rh --in
> rh_time_spval.mgh
> > --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster  --sum
> > rh_time_cluster_sum
> >
> >
> > Here is the error log:
> >
> > mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh
> > --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster  --sum
> > rh_time_cluster_sum thsign = pos, id = 1
> > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05
> greve Exp $
> > hemi   = rh
> > srcid  = rh_time_spval.mgh
> > srcsubjid  = fsaverage
> > srcsurf= white
> > srcframe   = 0
> > thsign = pos
> > thmin  = -1
> > thmax  = -1
> > fdr= 0.05
> > minarea= 0
> > xfmfile= talairach.xfm
> > nth = -1
> > outid= rh_time_cluster paint
> > sumfile  = rh_time_cluster_sum
> > subjectsdir= /gpfs/home/jtl190/work/structurals
> > FixMNI = 1
> > - XFM matrix (RAS2RAS) ---
> >
> /gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm
> >  1.000   0.000   0.000   0.000;
> >  0.000   1.000   0.000   0.000;
> >  0.000   0.000   1.000   0.000;
> >  0.000   0.000   0.000   1.000;
> > 
> > Reading source surface
> > /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white
> > Done reading source surface
> > Computing metric properties
> > Loading source values
> > number of voxels in search space = 163842
> > Done loading source values (nvtxs = 163842)
> > overall max = 1 at vertex 27
> > overall min = 1.52021e-05 at vertex 125620
> > surface nvertices 163842
> > surface area 65020.929688
> > surface area 65020.765625
> > Setting voxel-wise threshold with FDR = 0.05
> > Assuming input map is -log10(p)
> > MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=1.04576
> > FDR Voxel-wise threshold is 1.04576
> > Adjusting threshold for 1-tailed test.
> > If the input is not a -log10(p) volume, re-run with --no-adjust.
> > Searching for Clusters ...
> > thmin=1.045757 (0.744727), thmax=-1.00 (-1), thsignid=1,
> > minarea=0.00
> > Found 9803 clusters
> > Max cluster size 5993.586426
> > INFO: fixing MNI talairach coordinates
> > Saving thresholded output to  rh_time_cluster
> > Can't create file
> >
> /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.rh_time_cluster.w
> >
> > Permission denied
> >
> >
> >
> >
> > Thank you for taking the time to read this email.
> >
> > Sincerely,
> >
> > Jennifer Legault
> >
> > --
> > Jennifer Legault
> > Ph.D candidate, Neuroscience
> > Brain, Language, and Computation Lab
> > The Pennsylvania State University
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: 

[Freesurfer] Permission denied error with mri_surfcluster command

[Jennifer Legault]

Dear experts,

I am trying to use the cluster thresholding command for my freesurfer LME
outputs as referred to here
.  Any
feedback or comments would be greatly appreciated.

I am aware that there have been permission denied errors when using
mri_surfcluster and that applying this patch

should solve the problem (which I tried), however I am still either
receiving errors stating the permission is denied.

This is the command I am trying to run:

 mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh
--cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster  --sum
rh_time_cluster_sum


Here is the error log:

mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh
--cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster  --sum
rh_time_cluster_sum thsign = pos, id = 1
version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
hemi   = rh
srcid  = rh_time_spval.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = pos
thmin  = -1
thmax  = -1
fdr= 0.05
minarea= 0
xfmfile= talairach.xfm
nth = -1
outid= rh_time_cluster paint
sumfile  = rh_time_cluster_sum
subjectsdir= /gpfs/home/jtl190/work/structurals
FixMNI = 1
- XFM matrix (RAS2RAS) ---
/gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm
 1.000   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000;
 0.000   0.000   1.000   0.000;
 0.000   0.000   0.000   1.000;

Reading source surface
/gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white
Done reading source surface
Computing metric properties
Loading source values
number of voxels in search space = 163842
Done loading source values (nvtxs = 163842)
overall max = 1 at vertex 27
overall min = 1.52021e-05 at vertex 125620
surface nvertices 163842
surface area 65020.929688
surface area 65020.765625
Setting voxel-wise threshold with FDR = 0.05
Assuming input map is -log10(p)
MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=1.04576
FDR Voxel-wise threshold is 1.04576
Adjusting threshold for 1-tailed test.
If the input is not a -log10(p) volume, re-run with --no-adjust.
Searching for Clusters ...
thmin=1.045757 (0.744727), thmax=-1.00 (-1), thsignid=1,
minarea=0.00
Found 9803 clusters
Max cluster size 5993.586426
INFO: fixing MNI talairach coordinates
Saving thresholded output to  rh_time_cluster
Can't create file
/gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.rh_time_cluster.w

Permission denied




Thank you for taking the time to read this email.

Sincerely,

Jennifer Legault

-- 
Jennifer Legault
Ph.D candidate, Neuroscience
Brain, Language, and Computation Lab
The Pennsylvania State University
___
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Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Jennifer Legault]

Douglas,

Thank you for your quick response.  When I add --sd [path_location], I get
the following error:
Loading source values
mri_read(): couldn't determine type of file [path_location]/rh_time_spval
ERROR: could not read rh_time_spval as type

Should I use another argument?

Best,

Jen



On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve 
wrote:

> Try specifying the full path to the output
>
> On 02/10/2016 12:59 PM, Jennifer Legault wrote:
> > Dear experts,
> >
> > I am trying to use the cluster thresholding command for my freesurfer
> > LME outputs as referred to here
> > .
> > Any feedback or comments would be greatly appreciated.
> >
> > I am aware that there have been permission denied errors when using
> > mri_surfcluster and that applying this patch
> > <
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg
> >
> > should solve the problem (which I tried), however I am still either
> > receiving errors stating the permission is denied.
> >
> > This is the command I am trying to run:
> >
> >  mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh
> > --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster  --sum
> > rh_time_cluster_sum
> >
> >
> > Here is the error log:
> >
> > mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh
> > --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster  --sum
> > rh_time_cluster_sum thsign = pos, id = 1
> > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
> > hemi   = rh
> > srcid  = rh_time_spval.mgh
> > srcsubjid  = fsaverage
> > srcsurf= white
> > srcframe   = 0
> > thsign = pos
> > thmin  = -1
> > thmax  = -1
> > fdr= 0.05
> > minarea= 0
> > xfmfile= talairach.xfm
> > nth = -1
> > outid= rh_time_cluster paint
> > sumfile  = rh_time_cluster_sum
> > subjectsdir= /gpfs/home/jtl190/work/structurals
> > FixMNI = 1
> > - XFM matrix (RAS2RAS) ---
> > /gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm
> >  1.000   0.000   0.000   0.000;
> >  0.000   1.000   0.000   0.000;
> >  0.000   0.000   1.000   0.000;
> >  0.000   0.000   0.000   1.000;
> > 
> > Reading source surface
> > /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white
> > Done reading source surface
> > Computing metric properties
> > Loading source values
> > number of voxels in search space = 163842
> > Done loading source values (nvtxs = 163842)
> > overall max = 1 at vertex 27
> > overall min = 1.52021e-05 at vertex 125620
> > surface nvertices 163842
> > surface area 65020.929688
> > surface area 65020.765625
> > Setting voxel-wise threshold with FDR = 0.05
> > Assuming input map is -log10(p)
> > MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=1.04576
> > FDR Voxel-wise threshold is 1.04576
> > Adjusting threshold for 1-tailed test.
> > If the input is not a -log10(p) volume, re-run with --no-adjust.
> > Searching for Clusters ...
> > thmin=1.045757 (0.744727), thmax=-1.00 (-1), thsignid=1,
> > minarea=0.00
> > Found 9803 clusters
> > Max cluster size 5993.586426
> > INFO: fixing MNI talairach coordinates
> > Saving thresholded output to  rh_time_cluster
> > Can't create file
> > /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.rh_time_cluster.w
> >
> > Permission denied
> >
> >
> >
> >
> > Thank you for taking the time to read this email.
> >
> > Sincerely,
> >
> > Jennifer Legault
> >
> > --
> > Jennifer Legault
> > Ph.D candidate, Neuroscience
> > Brain, Language, and Computation Lab
> > The Pennsylvania State University
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>
> 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
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> properly
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Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Jennifer Legault]

Thank you very much for your help!  I still received a "cannot read file
type" error when I only added the path to the output --o part, however when
I also added the path to the input file, it worked!

I do have one more question: Which argument can I add so that in my output
file I see the clusterwise P value, like it is shown here

?

Best,

Jen

On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve 
wrote:

> I meant for the output files, so the --o in particular
>
> On 02/10/2016 01:47 PM, Jennifer Legault wrote:
> > Douglas,
> >
> > Thank you for your quick response.  When I add --sd [path_location], I
> > get the following error:
> > Loading source values
> > mri_read(): couldn't determine type of file [path_location]/rh_time_spval
> > ERROR: could not read rh_time_spval as type
> >
> > Should I use another argument?
> >
> > Best,
> >
> > Jen
> >
> >
> >
> > On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve
> > > wrote:
> >
> > Try specifying the full path to the output
> >
> > On 02/10/2016 12:59 PM, Jennifer Legault wrote:
> > > Dear experts,
> > >
> > > I am trying to use the cluster thresholding command for my
> > freesurfer
> > > LME outputs as referred to here
> > >
> >  >.
> > > Any feedback or comments would be greatly appreciated.
> > >
> > > I am aware that there have been permission denied errors when using
> > > mri_surfcluster and that applying this patch
> > >
> > <
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/mni152reg
> >
> > > should solve the problem (which I tried), however I am still either
> > > receiving errors stating the permission is denied.
> > >
> > > This is the command I am trying to run:
> > >
> > >  mri_surfcluster --subject fsaverage --hemi rh --in
> > rh_time_spval.mgh
> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster  --sum
> > > rh_time_cluster_sum
> > >
> > >
> > > Here is the error log:
> > >
> > > mri_surfcluster --subject fsaverage --hemi rh --in
> rh_time_spval.mgh
> > > --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster  --sum
> > > rh_time_cluster_sum thsign = pos, id = 1
> > > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05
> > greve Exp $
> > > hemi   = rh
> > > srcid  = rh_time_spval.mgh
> > > srcsubjid  = fsaverage
> > > srcsurf= white
> > > srcframe   = 0
> > > thsign = pos
> > > thmin  = -1
> > > thmax  = -1
> > > fdr= 0.05
> > > minarea= 0
> > > xfmfile= talairach.xfm
> > > nth = -1
> > > outid= rh_time_cluster paint
> > > sumfile  = rh_time_cluster_sum
> > > subjectsdir= /gpfs/home/jtl190/work/structurals
> > > FixMNI = 1
> > > - XFM matrix (RAS2RAS) ---
> > >
> >
>  /gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm
> > >  1.000   0.000   0.000   0.000;
> > >  0.000   1.000   0.000   0.000;
> > >  0.000   0.000   1.000   0.000;
> > >  0.000   0.000   0.000   1.000;
> > > 
> > > Reading source surface
> > > /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white
> > > Done reading source surface
> > > Computing metric properties
> > > Loading source values
> > > number of voxels in search space = 163842
> > > Done loading source values (nvtxs = 163842)
> > > overall max = 1 at vertex 27
> > > overall min = 1.52021e-05 at vertex 125620
> > > surface nvertices 163842
> > > surface area 65020.929688
> > > surface area 65020.765625
> > > Setting voxel-wise threshold with FDR = 0.05
> > > Assuming input map is -log10(p)
> > > MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=1.04576
> > > FDR Voxel-wise threshold is 1.04576
> > > Adjusting threshold for 1-tailed test.
> > > If the input is not a -log10(p) volume, re-run with --no-adjust.
> > > Searching for Clusters ...
> > > thmin=1.045757 (0.744727), thmax=-1.00 (-1), thsignid=1,
> > > minarea=0.00
> > > Found 9803 clusters
> > > Max cluster size 5993.586426
> > > INFO: fixing MNI talairach coordinates
> > > Saving thresholded output to  rh_time_cluster
> > > Can't create file
> > >
> >
>  /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.rh_time_cluster.w
> > >
> > > Permission denied
> > >
> > >
> > >
> > >
> > > Thank you for taking the time to read this email.
> > >
> > > Sincerely,
> > >
> > > Jennifer Legault
> > 

Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas N Greve]

Try specifying the full path to the output

On 02/10/2016 12:59 PM, Jennifer Legault wrote:
> Dear experts,
>
> I am trying to use the cluster thresholding command for my freesurfer 
> LME outputs as referred to here 
> . 
> Any feedback or comments would be greatly appreciated.
>
> I am aware that there have been permission denied errors when using 
> mri_surfcluster and that applying this patch 
>  
> should solve the problem (which I tried), however I am still either 
> receiving errors stating the permission is denied.
>
> This is the command I am trying to run:
>
>  mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh 
> --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster  --sum 
> rh_time_cluster_sum
>
>
> Here is the error log:
>
> mri_surfcluster --subject fsaverage --hemi rh --in rh_time_spval.mgh 
> --cwpvalthresh 0.05 --fdr .05 --sign pos --o rh_time_cluster  --sum 
> rh_time_cluster_sum thsign = pos, id = 1
> version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $
> hemi   = rh
> srcid  = rh_time_spval.mgh
> srcsubjid  = fsaverage
> srcsurf= white
> srcframe   = 0
> thsign = pos
> thmin  = -1
> thmax  = -1
> fdr= 0.05
> minarea= 0
> xfmfile= talairach.xfm
> nth = -1
> outid= rh_time_cluster paint
> sumfile  = rh_time_cluster_sum
> subjectsdir= /gpfs/home/jtl190/work/structurals
> FixMNI = 1
> - XFM matrix (RAS2RAS) ---
> /gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm
>  1.000   0.000   0.000   0.000;
>  0.000   1.000   0.000   0.000;
>  0.000   0.000   1.000   0.000;
>  0.000   0.000   0.000   1.000;
> 
> Reading source surface 
> /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white
> Done reading source surface
> Computing metric properties
> Loading source values
> number of voxels in search space = 163842
> Done loading source values (nvtxs = 163842)
> overall max = 1 at vertex 27
> overall min = 1.52021e-05 at vertex 125620
> surface nvertices 163842
> surface area 65020.929688
> surface area 65020.765625
> Setting voxel-wise threshold with FDR = 0.05
> Assuming input map is -log10(p)
> MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=1.04576
> FDR Voxel-wise threshold is 1.04576
> Adjusting threshold for 1-tailed test.
> If the input is not a -log10(p) volume, re-run with --no-adjust.
> Searching for Clusters ...
> thmin=1.045757 (0.744727), thmax=-1.00 (-1), thsignid=1, 
> minarea=0.00
> Found 9803 clusters
> Max cluster size 5993.586426
> INFO: fixing MNI talairach coordinates
> Saving thresholded output to  rh_time_cluster
> Can't create file 
> /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.rh_time_cluster.w
>
> Permission denied
>
>
>
>
> Thank you for taking the time to read this email.
>
> Sincerely,
>
> Jennifer Legault
>
> -- 
> Jennifer Legault
> Ph.D candidate, Neuroscience
> Brain, Language, and Computation Lab
> The Pennsylvania State University
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

___
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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.

Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas Greve]

There is a (very long) command line on that page. Mainly you need a csd 
file. To get that you need the FWHM of your analysis, the voxel-wise 
threshold, and the sign of the contrast (or abs). Then the relevant 
output will be the --sum. You can run it with --help to get more info.


On 2/10/16 5:11 PM, Jennifer Legault wrote:
Thank you very much for your help!  I still received a "cannot read 
file type" error when I only added the path to the output --o part, 
however when I also added the path to the input file, it worked!


I do have one more question: Which argument can I add so that in my 
output file I see the clusterwise P value, like it is shown here 
?


Best,

Jen

On Wed, Feb 10, 2016 at 1:50 PM, Douglas N Greve 
> wrote:


I meant for the output files, so the --o in particular

On 02/10/2016 01:47 PM, Jennifer Legault wrote:
> Douglas,
>
> Thank you for your quick response.  When I add --sd
[path_location], I
> get the following error:
> Loading source values
> mri_read(): couldn't determine type of file
[path_location]/rh_time_spval
> ERROR: could not read rh_time_spval as type
>
> Should I use another argument?
>
> Best,
>
> Jen
>
>
>
> On Wed, Feb 10, 2016 at 1:41 PM, Douglas N Greve
> 
>> wrote:
>
> Try specifying the full path to the output
>
> On 02/10/2016 12:59 PM, Jennifer Legault wrote:
> > Dear experts,
> >
> > I am trying to use the cluster thresholding command for my
> freesurfer
> > LME outputs as referred to here
> >
>   
 .

> > Any feedback or comments would be greatly appreciated.
> >
> > I am aware that there have been permission denied errors
when using
> > mri_surfcluster and that applying this patch
> >
>   
 

> > should solve the problem (which I tried), however I am
still either
> > receiving errors stating the permission is denied.
> >
> > This is the command I am trying to run:
> >
> >  mri_surfcluster --subject fsaverage --hemi rh --in
> rh_time_spval.mgh
> > --cwpvalthresh 0.05 --fdr .05 --sign pos --o
rh_time_cluster  --sum
> > rh_time_cluster_sum
> >
> >
> > Here is the error log:
> >
> > mri_surfcluster --subject fsaverage --hemi rh --in
rh_time_spval.mgh
> > --cwpvalthresh 0.05 --fdr .05 --sign pos --o
rh_time_cluster  --sum
> > rh_time_cluster_sum thsign = pos, id = 1
> > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05
> greve Exp $
> > hemi   = rh
> > srcid  = rh_time_spval.mgh
> > srcsubjid  = fsaverage
> > srcsurf= white
> > srcframe   = 0
> > thsign = pos
> > thmin  = -1
> > thmax  = -1
> > fdr= 0.05
> > minarea= 0
> > xfmfile= talairach.xfm
> > nth = -1
> > outid= rh_time_cluster paint
> > sumfile  = rh_time_cluster_sum
> > subjectsdir= /gpfs/home/jtl190/work/structurals
> > FixMNI = 1
> > - XFM matrix (RAS2RAS) ---
> >
>
 /gpfs/home/jtl190/work/structurals/fsaverage/mri/transforms/talairach.xfm
> >  1.000   0.000   0.000   0.000;
> >  0.000   1.000   0.000   0.000;
> >  0.000   0.000   1.000   0.000;
> >  0.000   0.000   0.000   1.000;
> > 
> > Reading source surface
> > /gpfs/home/jtl190/work/structurals/fsaverage/surf/rh.white
> > Done reading source surface
> > Computing metric properties
> > Loading source values
> > number of voxels in search space = 163842
> > Done loading source values (nvtxs = 163842)
> > overall max = 1 at vertex 27
> > overall min = 1.52021e-05 at vertex 125620
> > surface nvertices 163842
> > surface area 65020.929688
> > surface area 65020.765625
> > Setting voxel-wise threshold with FDR = 0.05
> > Assuming input map is -log10(p)
> > MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05,
vwth=1.04576
> > FDR Voxel-wise threshold is 1.04576
> > Adjusting threshold for 1-tailed test.
> > If the input is not a