Re: [Freesurfer] Permission denied mri_surf2surf

2020-09-09 Thread fsbuild
External Email - Use Caution

Hello Ellen,
I suspect that you really do not have the system privileges to read/write every 
subject directory. I have run into this with other commands that scan 
multiple subject directories.
Assuming there is one top level directory that contains all the subject 
directories, and it’s OK for you to try and set/change permissions on those 
files, then in terminal window you could “cd” to that parent directory,

$ cd path to top of tree containing all subject subdirectories
- and then try running the following command,
$ find . -maxdepth 1 -type d -exec chmod 755 {} \; -print
That will try and change the permissions of every subdirectory there such that 
you can read and write to it. But if you don’t have permission to access 
some of those directories, then you will get an error.. You may have to 
find someone wit, e.g., admin/root. privileges to change the permissions on the 
subdirectories the chmod command fails on.

- R.
On Sep 9, 2020, at 03:19, Ellen Ji ellen...@bli.uzh.ch 
wrote:External Email - Use Caution 
Dear experts,I created a loop for 
mri_surf2surf so that it would run for 300+subjects. For most of them, it 
ran successfully. However, it did notwork for 30 subjects. I then went to 
investigate one by one and I amgetting a Permission denied error for some 
reason. I confirm thatrecon-all has been performed and also that I have 
read/write/executepermissions. See below for the log. Any ideas why this 
could behappening to specific 
subjects? 
mri_surf2surf 
\
 --srcsubject fsaverage_sym 
\
 --trgsubject SPN01_CMH_0079_01 
\
 --hemi lh 
\
 --sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot 
\
 --tval SPN01_CMH_0079_01/label/lh.500_sym.aparc.annotSetting mapmethod to 
nnf7.1.0setenv SUBJECTS_DIR 
/home/eji/projects/spins/preproc/freesurfer/subjects/w0cd 
/home/eji/projects/spins/preproc/freesurfer/subjects/w0mri_surf2surf 
--srcsubject fsaverage_sym --trgsubject SPN01_CMH_0079_01--hemi lh 
--sval-annot fsaverage_sym/label/lh.500_sym.aparc.annot 
--tvalSPN01_CMH_0079_01/label/lh.500_sym.aparc.annotsysname 
Linuxhostname nu2machine x86_64user ejisrcsubject 
= fsaverage_symsrcval = (null)srctype 
=trgsubject = SPN01_CMH_0079_01trgval = 
SPN01_CMH_0079_01/label/lh.500_sym.aparc.annottrgtype 
=srcsurfreg = sphere.regtrgsurfreg = sphere.regsrchemi = 
lhtrghemi = lhframe = 
0fwhm-in = 0fwhm-out = 0label-src = 
(null)label-trg = (null)OKToRevFaceOrder = 1UseDualHemi = 0Reading 
source surface 
reg/home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.sphere.regLoading
 source dataReading surface 
file/home/eji/projects/spins/preproc/freesurfer/subjects/w0/fsaverage_sym/surf/lh.origreading
 colortable from annotation file...colortable with 161 entries read 
(originally/scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab)Reading 
target surface 
reg/home/eji/projects/spins/preproc/freesurfer/subjects/w0/SPN01_CMH_0079_01/surf/lh.sphere.regDoneUsing
 surf2surf_nnfr()Mapping Source Volume onto Source Subject 
Surfacesurf2surf_nnfr: building source hash (res=16).Surf2Surf: Forward Loop 
(123600)Surf2Surf: Dividing by number of hits (123600)INFO: nSrcLost = 
61776nTrg121 = 123600, nTrgMulti = 0, MnTrgMultiHits = 
0nSrc121 = 85136, nSrcLost = 61776, nSrcMulti = 78706, MnSrcMultiHits 
=0.488705Saving target dataConverting to target annotSaving to target 
annot SPN01_CMH_0079_01/label/lh.500_sym.aparc.annoterror: Permission 
deniederror: could not write annot 
fileSPN01_CMH_0079_01/label/lh.500_sym.aparc.annot___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-03-03 Thread 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

2016-03-03 Thread 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

2016-03-01 Thread 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

2016-02-25 Thread 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

2016-02-11 Thread 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

2016-02-11 Thread 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

2016-02-11 Thread 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

2016-02-11 Thread 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

2016-02-10 Thread 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: 

Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-10 Thread 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
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
> 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.
>
>



Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-10 Thread 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

2016-02-10 Thread 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/

___
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.



Re: [Freesurfer] Permission denied error with mri_surfcluster command

2016-02-10 Thread 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 

Re: [Freesurfer] permission denied

2014-11-04 Thread Robby De Pauw
Hi

I’ve previously encountered the same error. I’ve also tried to change 
permission but that didn’t really work out for me. I have fixed it by 
installing libjpeg62-dev: Maybe the following command could fix your problem 
too?

sudo apt-get install libjpeg62-dev

Hope this might work for you?

Cheers

Robby

Robby De Pauw, drs.
Ghent University
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent

robby.dep...@ugent.be






 On 31 Oct 2014, at 16:35, zkauf...@nmr.mgh.harvard.edu wrote:
 
 Yes, please try running as root and get back when you have the chance.
 This is a very odd issue and your results when running as root will
 provide insight.
 
 -Zeke
 
 Hi Z K,
 
 Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one
 installed with the latest freesurfer version did not work while others
 finished the processing in a reasonable processing time and I got the
 results.
 
 Also, I have a PC at my office installed with the latest freesurfer
 version
 and it works fine. So I have two PCs installed with the latest Freesurfer
 (one of them which does not work is in the lab).
 
 
 To summarize:
 All PCs (16 PCs in the lab and 1 in my office) are installed with latest
 Ubuntu version 14.04 64 bits
 15 PCs in the lab are installed with freesurfer 5.0.0 version
 1 PC in the lab is installed with the latest freesurfer version (does not
 work, permission denied)
 1 PC in my office is installed with the latest freesurfer version (works
 fine)
 
 All these PCs have Ubuntu 14.04 64bit installed on them.
 
 
 
 No, I am not using any vitual machine.
 
 Regarding the root user, I will try it on Sunday as I am away for a couple
 of days.
 
 Many thanks for your continuous support.
 
 Ali
 
 
 
 
 On Thu, Oct 30, 2014 at 6:34 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:
 
 Ali,
 
 First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are
 working properly? I am under the impression that versions of freesurfer
 pre-version 5.3 will not work on newer linux distributions?
 
 
 In regards to your current permision denied issue... What happens if you
 try and run tkmedit as root user? Also, you not using virtual machine
 setup are you?
 
 -Zeke
 
 On 10/30/2014 06:27 AM, Ali Radaideh wrote:
 It does not work. This is really strange
 
 On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu
 mailto:zkauf...@nmr.mgh.harvard.edu wrote:
 
I beleive it should have a lower case X, as in:
 
chmod -R a+x freesurfer/bin
 
-Zeke
 
On 10/28/2014 01:19 AM, Ali Radaideh wrote:
 Dear Douglas
 
 Thanks for your reply. unfortunatey I still get the same error.
Here is
 the terminal output. Is there anything else I can do?
 
  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 FREESURFER_HOME   /usr/local/freesurfer
 FSFAST_HOME   /usr/local/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii.gz
 SUBJECTS_DIR  /usr/local/freesurfer/subjects
 MNI_DIR   /usr/local/freesurfer/mni
 FSL_DIR   /usr/local/fsl
 imaging@imaging-ThinkCentre-23:~$ tcsh
 imaging-ThinkCentre-23:~ tkmedit
 /usr/local/freesurfer/bin/tkmedit: Permission denied.
 imaging-ThinkCentre-23:~
 
 
 On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu
mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
Try chmod -R a+X freesurfer/bin
 
 
On 10/26/14 1:57 PM, Ali Radaideh wrote:
Dear FreeSurfer users,
 
I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One
of the
PCs has the latest version of freesurfer 5.3.0 while the
 others
have the version 5.0.0. The PC that is installed with the
 latest
version freesurfer 5.3.0 does not allow me to run any
command and
everytime I try a command such such as tkmedit i get the
following
error
/usr/local/freesurfer/bin/tkmedit: permission denied.
 
I have tried to change the permission settings
sudo chown -R imaging:imaging freesurfer
 
but did not work.
 
Any ideas why is this happening although I have done the
 same
thing to other PCs and they are working fine.
 
​Thanks in advance,
Ali​
 
--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo 
 mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
/
/webpage:
 http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ 
 http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
 
 
 
___
Freesurfer mailing 

Re: [Freesurfer] permission denied

2014-10-31 Thread Ali Radaideh
Hi Z K,

Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one
installed with the latest freesurfer version did not work while others
finished the processing in a reasonable processing time and I got the
results.

Also, I have a PC at my office installed with the latest freesurfer version
and it works fine. So I have two PCs installed with the latest Freesurfer
(one of them which does not work is in the lab).


To summarize:
All PCs (16 PCs in the lab and 1 in my office) are installed with latest
Ubuntu version 14.04 64 bits
15 PCs in the lab are installed with freesurfer 5.0.0 version
1 PC in the lab is installed with the latest freesurfer version (does not
work, permission denied)
1 PC in my office is installed with the latest freesurfer version (works
fine)

All these PCs have Ubuntu 14.04 64bit installed on them.



No, I am not using any vitual machine.

Regarding the root user, I will try it on Sunday as I am away for a couple
of days.

Many thanks for your continuous support.

Ali




On Thu, Oct 30, 2014 at 6:34 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:

 Ali,

 First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are
 working properly? I am under the impression that versions of freesurfer
 pre-version 5.3 will not work on newer linux distributions?


 In regards to your current permision denied issue... What happens if you
 try and run tkmedit as root user? Also, you not using virtual machine
 setup are you?

 -Zeke

 On 10/30/2014 06:27 AM, Ali Radaideh wrote:
  It does not work. This is really strange
 
  On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu
  mailto:zkauf...@nmr.mgh.harvard.edu wrote:
 
  I beleive it should have a lower case X, as in:
 
  chmod -R a+x freesurfer/bin
 
  -Zeke
 
  On 10/28/2014 01:19 AM, Ali Radaideh wrote:
Dear Douglas
   
Thanks for your reply. unfortunatey I still get the same error.
  Here is
the terminal output. Is there anything else I can do?
   
 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl
imaging@imaging-ThinkCentre-23:~$ tcsh
imaging-ThinkCentre-23:~ tkmedit
/usr/local/freesurfer/bin/tkmedit: Permission denied.
imaging-ThinkCentre-23:~
   
   
On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu wrote:
   
   
Try chmod -R a+X freesurfer/bin
   
   
On 10/26/14 1:57 PM, Ali Radaideh wrote:
Dear FreeSurfer users,
   
I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One
  of the
PCs has the latest version of freesurfer 5.3.0 while the
 others
have the version 5.0.0. The PC that is installed with the
 latest
version freesurfer 5.3.0 does not allow me to run any
  command and
everytime I try a command such such as tkmedit i get the
  following
error
/usr/local/freesurfer/bin/tkmedit: permission denied.
   
I have tried to change the permission settings
sudo chown -R imaging:imaging freesurfer
   
but did not work.
   
Any ideas why is this happening although I have done the same
thing to other PCs and they are working fine.
   
​Thanks in advance,
Ali​
   
--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo
  mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  mailto:ali.radai...@hu.edu.jo
/
/webpage:
 http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
   
   
   
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Re: [Freesurfer] permission denied

2014-10-31 Thread zkaufman
Yes, please try running as root and get back when you have the chance.
This is a very odd issue and your results when running as root will
provide insight.

-Zeke

 Hi Z K,

 Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one
 installed with the latest freesurfer version did not work while others
 finished the processing in a reasonable processing time and I got the
 results.

 Also, I have a PC at my office installed with the latest freesurfer
 version
 and it works fine. So I have two PCs installed with the latest Freesurfer
 (one of them which does not work is in the lab).


 To summarize:
 All PCs (16 PCs in the lab and 1 in my office) are installed with latest
 Ubuntu version 14.04 64 bits
 15 PCs in the lab are installed with freesurfer 5.0.0 version
 1 PC in the lab is installed with the latest freesurfer version (does not
 work, permission denied)
 1 PC in my office is installed with the latest freesurfer version (works
 fine)

 All these PCs have Ubuntu 14.04 64bit installed on them.



 No, I am not using any vitual machine.

 Regarding the root user, I will try it on Sunday as I am away for a couple
 of days.

 Many thanks for your continuous support.

 Ali




 On Thu, Oct 30, 2014 at 6:34 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote:

 Ali,

 First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are
 working properly? I am under the impression that versions of freesurfer
 pre-version 5.3 will not work on newer linux distributions?


 In regards to your current permision denied issue... What happens if you
 try and run tkmedit as root user? Also, you not using virtual machine
 setup are you?

 -Zeke

 On 10/30/2014 06:27 AM, Ali Radaideh wrote:
  It does not work. This is really strange
 
  On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu
  mailto:zkauf...@nmr.mgh.harvard.edu wrote:
 
  I beleive it should have a lower case X, as in:
 
  chmod -R a+x freesurfer/bin
 
  -Zeke
 
  On 10/28/2014 01:19 AM, Ali Radaideh wrote:
Dear Douglas
   
Thanks for your reply. unfortunatey I still get the same error.
  Here is
the terminal output. Is there anything else I can do?
   
 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl
imaging@imaging-ThinkCentre-23:~$ tcsh
imaging-ThinkCentre-23:~ tkmedit
/usr/local/freesurfer/bin/tkmedit: Permission denied.
imaging-ThinkCentre-23:~
   
   
On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu
  mailto:gr...@nmr.mgh.harvard.edu wrote:
   
   
Try chmod -R a+X freesurfer/bin
   
   
On 10/26/14 1:57 PM, Ali Radaideh wrote:
Dear FreeSurfer users,
   
I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One
  of the
PCs has the latest version of freesurfer 5.3.0 while the
 others
have the version 5.0.0. The PC that is installed with the
 latest
version freesurfer 5.3.0 does not allow me to run any
  command and
everytime I try a command such such as tkmedit i get the
  following
error
/usr/local/freesurfer/bin/tkmedit: permission denied.
   
I have tried to change the permission settings
sudo chown -R imaging:imaging freesurfer
   
but did not work.
   
Any ideas why is this happening although I have done the
 same
thing to other PCs and they are working fine.
   
​Thanks in advance,
Ali​
   
--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo
  mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  mailto:ali.radai...@hu.edu.jo
/
/webpage:
 http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
   
   
   
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Re: [Freesurfer] permission denied

2014-10-30 Thread Ali Radaideh
It does not work. This is really strange

On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote:

 I beleive it should have a lower case X, as in:

 chmod -R a+x freesurfer/bin

 -Zeke

 On 10/28/2014 01:19 AM, Ali Radaideh wrote:
  Dear Douglas
 
  Thanks for your reply. unfortunatey I still get the same error. Here is
  the terminal output. Is there anything else I can do?
 
   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
  Setting up environment for FreeSurfer/FS-FAST (and FSL)
  FREESURFER_HOME   /usr/local/freesurfer
  FSFAST_HOME   /usr/local/freesurfer/fsfast
  FSF_OUTPUT_FORMAT nii.gz
  SUBJECTS_DIR  /usr/local/freesurfer/subjects
  MNI_DIR   /usr/local/freesurfer/mni
  FSL_DIR   /usr/local/fsl
  imaging@imaging-ThinkCentre-23:~$ tcsh
  imaging-ThinkCentre-23:~ tkmedit
  /usr/local/freesurfer/bin/tkmedit: Permission denied.
  imaging-ThinkCentre-23:~
 
 
  On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
  gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
  Try chmod -R a+X freesurfer/bin
 
 
  On 10/26/14 1:57 PM, Ali Radaideh wrote:
  Dear FreeSurfer users,
 
  I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the
  PCs has the latest version of freesurfer 5.3.0 while the others
  have the version 5.0.0. The PC that is installed with the latest
  version freesurfer 5.3.0 does not allow me to run any command and
  everytime I try a command such such as tkmedit i get the following
  error
  /usr/local/freesurfer/bin/tkmedit: permission denied.
 
  I have tried to change the permission settings
  sudo chown -R imaging:imaging freesurfer
 
  but did not work.
 
  Any ideas why is this happening although I have done the same
  thing to other PCs and they are working fine.
 
  ​Thanks in advance,
  Ali​
 
  --
  /Ali M. Al-Radaideh. PhD
  Assistant Professor
  Head of Department of Medical Imaging
  Vice Dean of the Faculty of Allied Health Sciences
  The Hashemite University,
  Zarqa, Jordan
  W.phone +962 5 390 ext.5422, 5355, 5364
  Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  /
  /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
 
 
 
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 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.
 
 
 
 
  --
  /Ali M. Al-Radaideh. PhD
  Assistant Professor
  Head of Department of Medical Imaging
  Vice Dean of the Faculty of Allied Health Sciences
  The Hashemite University,
  Zarqa, Jordan
  W.phone +962 5 390 ext.5422, 5355, 5364
  Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  /
  /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
 
 
 
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-- 








*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical
ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite
University, Zarqa, JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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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

2014-10-30 Thread Z K
Ali,

First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are 
working properly? I am under the impression that versions of freesurfer 
pre-version 5.3 will not work on newer linux distributions?


In regards to your current permision denied issue... What happens if you 
try and run tkmedit as root user? Also, you not using virtual machine 
setup are you?

-Zeke

On 10/30/2014 06:27 AM, Ali Radaideh wrote:
 It does not work. This is really strange

 On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu
 mailto:zkauf...@nmr.mgh.harvard.edu wrote:

 I beleive it should have a lower case X, as in:

 chmod -R a+x freesurfer/bin

 -Zeke

 On 10/28/2014 01:19 AM, Ali Radaideh wrote:
   Dear Douglas
  
   Thanks for your reply. unfortunatey I still get the same error.
 Here is
   the terminal output. Is there anything else I can do?
  
    freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
   Setting up environment for FreeSurfer/FS-FAST (and FSL)
   FREESURFER_HOME   /usr/local/freesurfer
   FSFAST_HOME   /usr/local/freesurfer/fsfast
   FSF_OUTPUT_FORMAT nii.gz
   SUBJECTS_DIR  /usr/local/freesurfer/subjects
   MNI_DIR   /usr/local/freesurfer/mni
   FSL_DIR   /usr/local/fsl
   imaging@imaging-ThinkCentre-23:~$ tcsh
   imaging-ThinkCentre-23:~ tkmedit
   /usr/local/freesurfer/bin/tkmedit: Permission denied.
   imaging-ThinkCentre-23:~
  
  
   On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
   gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:
  
  
   Try chmod -R a+X freesurfer/bin
  
  
   On 10/26/14 1:57 PM, Ali Radaideh wrote:
   Dear FreeSurfer users,
  
   I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One
 of the
   PCs has the latest version of freesurfer 5.3.0 while the others
   have the version 5.0.0. The PC that is installed with the latest
   version freesurfer 5.3.0 does not allow me to run any
 command and
   everytime I try a command such such as tkmedit i get the
 following
   error
   /usr/local/freesurfer/bin/tkmedit: permission denied.
  
   I have tried to change the permission settings
   sudo chown -R imaging:imaging freesurfer
  
   but did not work.
  
   Any ideas why is this happening although I have done the same
   thing to other PCs and they are working fine.
  
   ​Thanks in advance,
   Ali​
  
   --
   /Ali M. Al-Radaideh. PhD
   Assistant Professor
   Head of Department of Medical Imaging
   Vice Dean of the Faculty of Allied Health Sciences
   The Hashemite University,
   Zarqa, Jordan
   W.phone +962 5 390 ext.5422, 5355, 5364
   Email: ali.radai...@hu.edu.jo
 mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
 mailto:ali.radai...@hu.edu.jo
   /
   /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
  
  
  
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 mailto:Freesurfer@nmr.mgh.harvard.edu
 mailto: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.
  
  
  
  
   --
   /Ali M. Al-Radaideh. PhD
   Assistant Professor
   Head of Department of Medical Imaging
   Vice Dean of the Faculty of Allied Health Sciences
   The Hashemite University,
   Zarqa, Jordan
   W.phone +962 5 390 ext.5422, 5355, 5364
   Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
 mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
   /
   /webpage: 

Re: [Freesurfer] permission denied

2014-10-30 Thread Douglas N Greve

Try this
chmod -R a+x freesurfer/bin/*

On 10/30/2014 06:27 AM, Ali Radaideh wrote:
 It does not work. This is really strange

 On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu 
 mailto:zkauf...@nmr.mgh.harvard.edu wrote:

 I beleive it should have a lower case X, as in:

 chmod -R a+x freesurfer/bin

 -Zeke

 On 10/28/2014 01:19 AM, Ali Radaideh wrote:
  Dear Douglas
 
  Thanks for your reply. unfortunatey I still get the same error.
 Here is
  the terminal output. Is there anything else I can do?
 
   freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
  Setting up environment for FreeSurfer/FS-FAST (and FSL)
  FREESURFER_HOME /usr/local/freesurfer
  FSFAST_HOME /usr/local/freesurfer/fsfast
  FSF_OUTPUT_FORMAT nii.gz
  SUBJECTS_DIR /usr/local/freesurfer/subjects
  MNI_DIR /usr/local/freesurfer/mni
  FSL_DIR /usr/local/fsl
  imaging@imaging-ThinkCentre-23:~$ tcsh
  imaging-ThinkCentre-23:~ tkmedit
  /usr/local/freesurfer/bin/tkmedit: Permission denied.
  imaging-ThinkCentre-23:~
 
 
  On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
  gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu
 mailto:gr...@nmr.mgh.harvard.edu wrote:
 
 
  Try chmod -R a+X freesurfer/bin
 
 
  On 10/26/14 1:57 PM, Ali Radaideh wrote:
  Dear FreeSurfer users,
 
  I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the
  PCs has the latest version of freesurfer 5.3.0 while the others
  have the version 5.0.0. The PC that is installed with the latest
  version freesurfer 5.3.0 does not allow me to run any command and
  everytime I try a command such such as tkmedit i get the following
  error
  /usr/local/freesurfer/bin/tkmedit: permission denied.
 
  I have tried to change the permission settings
  sudo chown -R imaging:imaging freesurfer
 
  but did not work.
 
  Any ideas why is this happening although I have done the same
  thing to other PCs and they are working fine.
 
  ​Thanks in advance,
  Ali​
 
  --
  /Ali M. Al-Radaideh. PhD
  Assistant Professor
  Head of Department of Medical Imaging
  Vice Dean of the Faculty of Allied Health Sciences
  The Hashemite University,
  Zarqa, Jordan
  W.phone +962 5 390 ext.5422, 5355, 5364
  Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
 mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  /
  /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
 
 
 
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 mailto:Freesurfer@nmr.mgh.harvard.edu
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  ___
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  Freesurfer@nmr.mgh.harvard.edu
 mailto:Freesurfer@nmr.mgh.harvard.edu
 mailto:Freesurfer@nmr.mgh.harvard.edu
 mailto: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.
 
 
 
 
  --
  /Ali M. Al-Radaideh. PhD
  Assistant Professor
  Head of Department of Medical Imaging
  Vice Dean of the Faculty of Allied Health Sciences
  The Hashemite University,
  Zarqa, Jordan
  W.phone +962 5 390 ext.5422, 5355, 5364
  Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
 mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
  /
  /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/
 
 
 
  ___
  Freesurfer mailing list
  Freesurfer@nmr.mgh.harvard.edu
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 -- 
 /Ali M. Al-Radaideh. PhD
 Assistant Professor
 Head ofDepartment of Medical Imaging
 Vice Dean of the Faculty of Allied Health Sciences
 The Hashemite 

Re: [Freesurfer] permission denied

2014-10-29 Thread Z K
I beleive it should have a lower case X, as in:

chmod -R a+x freesurfer/bin

-Zeke

On 10/28/2014 01:19 AM, Ali Radaideh wrote:
 Dear Douglas

 Thanks for your reply. unfortunatey I still get the same error. Here is
 the terminal output. Is there anything else I can do?

  freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
 Setting up environment for FreeSurfer/FS-FAST (and FSL)
 FREESURFER_HOME   /usr/local/freesurfer
 FSFAST_HOME   /usr/local/freesurfer/fsfast
 FSF_OUTPUT_FORMAT nii.gz
 SUBJECTS_DIR  /usr/local/freesurfer/subjects
 MNI_DIR   /usr/local/freesurfer/mni
 FSL_DIR   /usr/local/fsl
 imaging@imaging-ThinkCentre-23:~$ tcsh
 imaging-ThinkCentre-23:~ tkmedit
 /usr/local/freesurfer/bin/tkmedit: Permission denied.
 imaging-ThinkCentre-23:~


 On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve
 gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:


 Try chmod -R a+X freesurfer/bin


 On 10/26/14 1:57 PM, Ali Radaideh wrote:
 Dear FreeSurfer users,

 I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the
 PCs has the latest version of freesurfer 5.3.0 while the others
 have the version 5.0.0. The PC that is installed with the latest
 version freesurfer 5.3.0 does not allow me to run any command and
 everytime I try a command such such as tkmedit i get the following
 error
 /usr/local/freesurfer/bin/tkmedit: permission denied.

 I have tried to change the permission settings
 sudo chown -R imaging:imaging freesurfer

 but did not work.

 Any ideas why is this happening although I have done the same
 thing to other PCs and they are working fine.

 ​Thanks in advance,
 Ali​

 --
 /Ali M. Al-Radaideh. PhD
 Assistant Professor
 Head of Department of Medical Imaging
 Vice Dean of the Faculty of Allied Health Sciences
 The Hashemite University,
 Zarqa, Jordan
 W.phone +962 5 390 ext.5422, 5355, 5364
 Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
 /
 /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/



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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.




 --
 /Ali M. Al-Radaideh. PhD
 Assistant Professor
 Head of Department of Medical Imaging
 Vice Dean of the Faculty of Allied Health Sciences
 The Hashemite University,
 Zarqa, Jordan
 W.phone +962 5 390 ext.5422, 5355, 5364
 Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
 /
 /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/



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Re: [Freesurfer] permission denied

2014-10-27 Thread Ali Radaideh
Dear Douglas

Thanks for your reply. unfortunatey I still get the same error. Here is the
terminal output. Is there anything else I can do?

 freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME   /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /usr/local/freesurfer/subjects
MNI_DIR   /usr/local/freesurfer/mni
FSL_DIR   /usr/local/fsl
imaging@imaging-ThinkCentre-23:~$ tcsh
imaging-ThinkCentre-23:~ tkmedit
/usr/local/freesurfer/bin/tkmedit: Permission denied.
imaging-ThinkCentre-23:~


On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:


 Try chmod -R a+X freesurfer/bin


 On 10/26/14 1:57 PM, Ali Radaideh wrote:

  Dear FreeSurfer users,

  I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs
 has the latest version of freesurfer 5.3.0 while the others have the
 version 5.0.0. The PC that is installed with the latest version freesurfer
 5.3.0 does not allow me to run any command and everytime I try a command
 such such as tkmedit i get the following error
 /usr/local/freesurfer/bin/tkmedit: permission denied.

  I have tried to change the permission settings
 sudo chown -R imaging:imaging freesurfer

  but did not work.

  Any ideas why is this happening although I have done the same thing to
 other PCs and they are working fine.

  ​Thanks in advance,
 Ali​

  --








 *Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical
 Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite
 University,  Zarqa, Jordan W.phone +962 5 390 ext.5422, 5355, 5364
 Email: ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo *
 *webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
 http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*



 ___
 Freesurfer mailing 
 listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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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.




-- 








*Ali M. Al-Radaideh. PhDAssistant ProfessorHead of Department of Medical
ImagingVice Dean of the Faculty of Allied Health SciencesThe Hashemite
University, Zarqa, JordanW.phone +962 5 390 ext.5422, 5355, 5364Email:
ali.radai...@hu.edu.jo ali.radai...@hu.edu.jo*
*webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=
http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=*
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] permission denied

2014-10-26 Thread Douglas Greve


Try chmod -R a+X freesurfer/bin


On 10/26/14 1:57 PM, Ali Radaideh wrote:

Dear FreeSurfer users,

I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs 
has the latest version of freesurfer 5.3.0 while the others have the 
version 5.0.0. The PC that is installed with the latest version 
freesurfer 5.3.0 does not allow me to run any command and everytime I 
try a command such such as tkmedit i get the following error

/usr/local/freesurfer/bin/tkmedit: permission denied.

I have tried to change the permission settings
sudo chown -R imaging:imaging freesurfer

but did not work.

Any ideas why is this happening although I have done the same thing to 
other PCs and they are working fine.


Thanks in advance,
Ali

--
/Ali M. Al-Radaideh. PhD
Assistant Professor
Head of Department of Medical Imaging
Vice Dean of the Faculty of Allied Health Sciences
The Hashemite University,
Zarqa, Jordan
W.phone +962 5 390 ext.5422, 5355, 5364
Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo
/
/webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/



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Re: [Freesurfer] Permission denied

2013-03-14 Thread Bruce Fischl
you probably want to specify the SUBJECTS_DIR as being somewhere else 
that you have write permission to. You can do this with the -sd path on 
the recon-all command line, or in the environment.


cheers
Bruce
On Thu, 14 Mar 2013, 
Varghese Chikku wrote:



Dear FS team,I dowloaded the latest ML  version of  FS and tried to run a
 subject.But this  error is coming up.Any  suggestions?

 chikkuvarghese$ recon-all -i
/Users/chikkuvarghese/Desktop/BL/raw/image1 -autorecon-all -s BL1
mkdir: /Applications/freesurfer/subjects/BL1: Permission denied
mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied
mkdir: /Applications/freesurfer/subjects/BL1/scripts: Permission denied
cp: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such
file or directory
cat: /Applications/freesurfer/subjects/BL1/scripts/build-stamp.txt: No such
file or directory
INFO: FreeSurfer build stamps do not match
Subject Stamp: 
Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0
INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects
Actual FREESURFER_HOME /Applications/freesurfer
/Applications/freesurfer/subjects/BL1: No such file or directory.
chikkus-MacBook-Pro:~ chikkuvarghese$ 


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Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

2013-03-11 Thread Anastasia Yendiki

Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or 
is BA3b.thresh the only one? If you remove the .thresh do you still get an 
error?

Thanks,
a.y

On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:

 Hello,

 I ran recon-all and left it running Friday afternoon/evening. When I next
 checked it this morning, the script had finished with errors. Looks like
 there was a problem with the file:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

 /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is a
 symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage

 Seems like I should be able to read lh.BA3b.thresh.label. Not sure why the
 script couldn't open it. Thoughts?

 -Ronny

 Further info below:

 machine: quito
 Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308
 /usr/local/freesurfer/dev/bin/freesurfer
 SUBJECTS_DIR:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
 Working Directory:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig

 ** the exact command line I ran
 recon-all -autorecon2-cp -autorecon3 -subjid subj004

 ** The command that caused the error (which was as a part of/ within the
 recon-all script) is
 mri_label2label --srcsubject fsaverage --srclabel
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
 --regmethod surface

 ** ERROR MESSAGE RECEIVED **
 Permission denied
 mri_label2label: could not open label file
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

 srclabel =
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 srcsubject = fsaverage
 trgsubject = subj004
 trglabel = ./lh.BA3b.thresh.label
 regmethod = surface

 srchemi = lh
 trghemi = lh
 trgsurface = white
 srcsurfreg = sphere.reg
 trgsurfreg = sphere.reg
 usehash = 1
 Use ProjAbs  = 0, 0
 Use ProjFrac = 0, 0
 DoPaint 0

 SUBJECTS_DIR
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
 FREESURFER_HOME /usr/local/freesurfer/dev
 Loading source label.
 Invalid argument
 ERROR reading
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013
 x86_64 x86_64 x86_64 GNU/Linux

 recon-all -s subj004 exited with ERRORS at Fri Mar  8 21:04:18 EST 2013

 For more details, see the log file
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log
 To report a problem, see
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.



Re: [Freesurfer] Permission denied - could not open lh.BA3b.thresh.label

2013-03-11 Thread preciado
It looks like this is the first *thresh.* label that caused the problem.
The following command ran and executed properly just before the error
message on the log.

 mri_label2label --srcsubject fsaverage --srclabel
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label
--trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh
--regmethod surface

So looks like lh.BA3a.thresh.label ran just fine, but not
lh.BA3b.thresh.label. This ran as part of recon-all and failed in the
middle of executing that script so I hadn't even tried to run it any other
way (without *.thresh.*)

That said, I just ran the problematic piece line of code and it all of a
sudden works just fine...
mri_label2label --srcsubject fsaverage --srclabel
/autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
--trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
--regmethod surface

Any reason why it wouldn't have worked Friday near 7pm and works not?

-Ronny


 Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or
 is BA3b.thresh the only one? If you remove the .thresh do you still get an
 error?

 Thanks,
 a.y

 On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:

 Hello,

 I ran recon-all and left it running Friday afternoon/evening. When I
 next
 checked it this morning, the script had finished with errors. Looks like
 there was a problem with the file:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

 /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is
 a
 symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage

 Seems like I should be able to read lh.BA3b.thresh.label. Not sure why
 the
 script couldn't open it. Thoughts?

 -Ronny

 Further info below:

 machine: quito
 Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308
 /usr/local/freesurfer/dev/bin/freesurfer
 SUBJECTS_DIR:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
 Working Directory:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig

 ** the exact command line I ran
 recon-all -autorecon2-cp -autorecon3 -subjid subj004

 ** The command that caused the error (which was as a part of/ within the
 recon-all script) is
 mri_label2label --srcsubject fsaverage --srclabel
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
 --regmethod surface

 ** ERROR MESSAGE RECEIVED **
 Permission denied
 mri_label2label: could not open label file
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

 srclabel =
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 srcsubject = fsaverage
 trgsubject = subj004
 trglabel = ./lh.BA3b.thresh.label
 regmethod = surface

 srchemi = lh
 trghemi = lh
 trgsurface = white
 srcsurfreg = sphere.reg
 trgsurfreg = sphere.reg
 usehash = 1
 Use ProjAbs  = 0, 0
 Use ProjFrac = 0, 0
 DoPaint 0

 SUBJECTS_DIR
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
 FREESURFER_HOME /usr/local/freesurfer/dev
 Loading source label.
 Invalid argument
 ERROR reading
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC
 2013
 x86_64 x86_64 x86_64 GNU/Linux

 recon-all -s subj004 exited with ERRORS at Fri Mar  8 21:04:18 EST 2013

 For more details, see the log file
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log
 To report a problem, see
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer







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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 - could not open lh.BA3b.thresh.label

2013-03-11 Thread Anastasia Yendiki

Probably a network glitch? I'd try restarting it and seeing if the error 
persists.

On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:

 It looks like this is the first *thresh.* label that caused the problem.
 The following command ran and executed properly just before the error
 message on the log.

 mri_label2label --srcsubject fsaverage --srclabel
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label
 --trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh
 --regmethod surface

 So looks like lh.BA3a.thresh.label ran just fine, but not
 lh.BA3b.thresh.label. This ran as part of recon-all and failed in the
 middle of executing that script so I hadn't even tried to run it any other
 way (without *.thresh.*)

 That said, I just ran the problematic piece line of code and it all of a
 sudden works just fine...
 mri_label2label --srcsubject fsaverage --srclabel
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
 --regmethod surface

 Any reason why it wouldn't have worked Friday near 7pm and works not?

 -Ronny


 Hi Ronny - Do you get errors with any other of the *.thresh.* labels? Or
 is BA3b.thresh the only one? If you remove the .thresh do you still get an
 error?

 Thanks,
 a.y

 On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:

 Hello,

 I ran recon-all and left it running Friday afternoon/evening. When I
 next
 checked it this morning, the script had finished with errors. Looks like
 there was a problem with the file:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

 /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage is
 a
 symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage

 Seems like I should be able to read lh.BA3b.thresh.label. Not sure why
 the
 script couldn't open it. Thoughts?

 -Ronny

 Further info below:

 machine: quito
 Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308
 /usr/local/freesurfer/dev/bin/freesurfer
 SUBJECTS_DIR:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
 Working Directory:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig

 ** the exact command line I ran
 recon-all -autorecon2-cp -autorecon3 -subjid subj004

 ** The command that caused the error (which was as a part of/ within the
 recon-all script) is
 mri_label2label --srcsubject fsaverage --srclabel
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
 --regmethod surface

 ** ERROR MESSAGE RECEIVED **
 Permission denied
 mri_label2label: could not open label file
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

 srclabel =
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 srcsubject = fsaverage
 trgsubject = subj004
 trglabel = ./lh.BA3b.thresh.label
 regmethod = surface

 srchemi = lh
 trghemi = lh
 trgsurface = white
 srcsurfreg = sphere.reg
 trgsurfreg = sphere.reg
 usehash = 1
 Use ProjAbs  = 0, 0
 Use ProjFrac = 0, 0
 DoPaint 0

 SUBJECTS_DIR
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
 FREESURFER_HOME /usr/local/freesurfer/dev
 Loading source label.
 Invalid argument
 ERROR reading
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC
 2013
 x86_64 x86_64 x86_64 GNU/Linux

 recon-all -s subj004 exited with ERRORS at Fri Mar  8 21:04:18 EST 2013

 For more details, see the log file
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log
 To report a problem, see
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer









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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 - could not open lh.BA3b.thresh.label

2013-03-11 Thread preciado
I am thinking that that's possible. Same command with same type of
parameters executed successfully before the failure, and now previously
failed command is working. I will try it again...

Thanks for the input.

-Ronny


 Probably a network glitch? I'd try restarting it and seeing if the error
 persists.

 On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:

 It looks like this is the first *thresh.* label that caused the problem.
 The following command ran and executed properly just before the error
 message on the log.

 mri_label2label --srcsubject fsaverage --srclabel
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3a.thresh.label
 --trgsubject subj004 --trglabel ./lh.BA3a.thresh.label --hemi lh
 --regmethod surface

 So looks like lh.BA3a.thresh.label ran just fine, but not
 lh.BA3b.thresh.label. This ran as part of recon-all and failed in the
 middle of executing that script so I hadn't even tried to run it any
 other
 way (without *.thresh.*)

 That said, I just ran the problematic piece line of code and it all of a
 sudden works just fine...
 mri_label2label --srcsubject fsaverage --srclabel
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
 --regmethod surface

 Any reason why it wouldn't have worked Friday near 7pm and works not?

 -Ronny


 Hi Ronny - Do you get errors with any other of the *.thresh.* labels?
 Or
 is BA3b.thresh the only one? If you remove the .thresh do you still get
 an
 error?

 Thanks,
 a.y

 On Mon, 11 Mar 2013, preci...@nmr.mgh.harvard.edu wrote:

 Hello,

 I ran recon-all and left it running Friday afternoon/evening. When I
 next
 checked it this morning, the script had finished with errors. Looks
 like
 there was a problem with the file:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

 /cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage
 is
 a
 symlink to /cluster/freesurfer/centos6_x86_64/dev/subjects/fsaverage

 Seems like I should be able to read lh.BA3b.thresh.label. Not sure why
 the
 script couldn't open it. Thoughts?

 -Ronny

 Further info below:

 machine: quito
 Freesurfer vesion: freesurfer-Linux-centos6_x86_64-dev-20130308
 /usr/local/freesurfer/dev/bin/freesurfer
 SUBJECTS_DIR:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
 Working Directory:
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/mri/orig

 ** the exact command line I ran
 recon-all -autorecon2-cp -autorecon3 -subjid subj004

 ** The command that caused the error (which was as a part of/ within
 the
 recon-all script) is
 mri_label2label --srcsubject fsaverage --srclabel
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 --trgsubject subj004 --trglabel ./lh.BA3b.thresh.label --hemi lh
 --regmethod surface

 ** ERROR MESSAGE RECEIVED **
 Permission denied
 mri_label2label: could not open label file
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label

 srclabel =
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 srcsubject = fsaverage
 trgsubject = subj004
 trglabel = ./lh.BA3b.thresh.label
 regmethod = surface

 srchemi = lh
 trghemi = lh
 trgsurface = white
 srcsurfreg = sphere.reg
 trgsurfreg = sphere.reg
 usehash = 1
 Use ProjAbs  = 0, 0
 Use ProjFrac = 0, 0
 DoPaint 0

 SUBJECTS_DIR
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects
 FREESURFER_HOME /usr/local/freesurfer/dev
 Loading source label.
 Invalid argument
 ERROR reading
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.BA3b.thresh.label
 Linux quito 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC
 2013
 x86_64 x86_64 x86_64 GNU/Linux

 recon-all -s subj004 exited with ERRORS at Fri Mar  8 21:04:18 EST
 2013

 For more details, see the log file
 /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj004/scripts/recon-all.log
 To report a problem, see
 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Permission denied

2005-08-19 Thread Kevin Teich

Recently moved freesurfer from one system to another, but I am having
trouble executing it.

./csurf: Permission denied.
I have license in the right folder. Has anyone experienced the same
problem.


Make sure it is executable. Try:

chmod a+x csurf

--
Kevin Teich

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