Re: [Freesurfer] FS 5.3 and OS X 10.11

[Z K]

Testing freesurfer with the latest version of OSX is ongoing. Ive 
updated the message to state that "In some cases" freesurfer may fail 
when running version 5.3 on the lastest version of OSX. The cases where 
it does fail should be obvious, with an error message is output to the 
screen. If your recons are running to completion than you are all set. 
Thanks for pointing that out.

-Zeke

On 02/09/2016 08:34 PM, prasser wrote:
>
> Hi,
>
> On the download page it mentions that Freesurfer v5.3 is not compatible
> with OS X 10.11 because of an implementation of SIP. As a test, I have
> run a few subjects with v5.3 under OS X 10.11.3 with SIP enabled but was
> unable to see any problems, with all test subjects completing without error.
> I was wondering what I should be looking for (i.e. in the .log etc?)
> that would indicate that v5.3 is not compatible with OS X 10.11.3.
>
> Thanks.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] Free surfer- correcting for head size

[Martin Reuter]

Hi Chistina,

the aseg.stats has all that information. You can create a table from all 
subjects with asegstats2table . It will also contain the ICV (probably 
called eTIV or something like that). And you can use it in your model, 
which is probably the best approach.

Cheers, Martin


On 01/24/2016 02:58 PM, Christina van den Brink wrote:
> Hi Bruce (and the freesurfer community),
>
> Thanks for your reply! Would it be possible to get more details on the 
> process of how I might go about correcting these volumes myself? It would be 
> ideal if I had the volumes prior to entering it into my statistical model 
> (and thus I’d prefer not to use head size as a regressor if possible). When 
> you say ‘dividing it out’, is this simply taking the regional volumes and 
> dividing it by eTIV to obtain a proportion? What are the downsides to 
> approaching it in this manner vs. using it as a regressor?
>
> Many thanks,
>
> Christina
>
>
>
>> On Jan 11, 2016, at 12:46 PM, Bruce Fischl  
>> wrote:
>>
>> Hi Christina
>>
>> we don't correct any volumes for head size - we just provide the information 
>> for you to do it yourself. I think including it as a regressor is more 
>> common than dividing it out, but perhaps others can comment.
>>
>> cheers
>> Bruce
>> On Mon, 11 Jan 2016, Christina van den Brink wrote:
>>
>>> Hello,
>>> I have a question regarding volume-correction for the morphometry stats
>>> obtained via recon-all. I’ve noted that eTIV is derived using the atlas
>>> scaling factor in order to account for head size. I’m wondering whether the
>>> other volumes given, e.g. TotalGray or lhCorticalWhiteMatter, have also been
>>> corrected for head size? If not, is there a recommended method in which to
>>> do so so that regional volumes can be compared between participants?
>>> Many thanks for your help!
>>> Best,
>>> Christina
>> ___
>> 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.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu

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

[Freesurfer] Middle cerebellar peduncle segmentation

[Henri Pazro]

Dear experts,

I'm trying the brainstem segmentation from Juan Eugenio Iglesias and would
like to know if the middle cerebellar peduncle will be added in a near
future?

Thanks!

H.
___
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] pial edits in subject with severe atrophy

[Bruce Fischl]

Sorry Corinna

I meant to answer this the first time but it slipped through the cracks. 
I doubt there is much you can do if there is that big a lesion. If the 
topology is wrong and you can't see tissue in those regions it's going to 
be very hard
Bruce


On Wed, 10 Feb 2016, 
Corinna Bauer wrote:

> Dear Experts,
> 
> I have a subject with severe atrophy in bilateral frontal and parietal
> regions and after many rounds of edits to the brainmask, wm.mgz, and control
> points, these regions are still left uncaptured. Is there a way to edit the
> pial surface to include these grey matter regions? I am hesitant to draw
> them in via the wm surface since there is no definite WM present.
> 
> I do have a FLAIR also on this subject.
> 
> I've attached a couple examples.
> 
> Thanks!
> 
> Corinna
> 
>
___
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.

[Freesurfer] pial edits in subject with severe atrophy

[Corinna Bauer]

Dear Experts,

I have a subject with severe atrophy in bilateral frontal and parietal
regions and after many rounds of edits to the brainmask, wm.mgz, and
control points, these regions are still left uncaptured. Is there a way to
edit the pial surface to include these grey matter regions? I am hesitant
to draw them in via the wm surface since there is no definite WM present.

I do have a FLAIR also on this subject.

I've attached a couple examples.

Thanks!

Corinna
___
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] error in motion correction

[Ji Won Bang]

Dear. Freesurfer team.

Thanks so much your help and advice.

Based on the comments, I'm trying freesurfer version 5.3.0 instead of 4.5.0
now.

In our experiment, each participant is scanned twice on different days and
the functional scan's brain volume are different (some scans have 33 number
of slices, some have 32 number of slices).

Since participants moved a bit between scans on the same day, and the head
position is different between different days, my advisor advised me to do
co-registration between different functional scans and then do
co-registration between anatomical and functional scans.

My question is this.

If I do motion-correction such that we align all EPI data to the first EPI
of the first functional scan, will it be enough for co-registration between
different functional scans and different days? Or should I do
coregistration-specific process such as mri_robust_register,
mri_robust_template etc?

Or I guess the method I choose should depend on how much the participant
moved between scans and how much different the head position was between
different days? For example, if the participant was very still between runs
and the head position was not that too different, this motion correction is
enough for coregistration between functional scans. However, if not, I
should do coregistration-specific process such as mri_robust_register,
mri_robust_template etc?

I'd appreciate any of your advice.

Please feel free to let me know your thoughts.

Best,
Ji Won

2016-02-08 22:31 GMT-05:00 Douglas Greve :

> In 4.5 I don't think there is a way to run it when different runs have
> different number of slices. Version 5+ will handle it properly. If you
> really want to use 4.5, then you'll have to put it in a different
> functional subdir (FSD, eg, bold), and create a new analysis for it, then
> combine them together after analysis. A bit of a hassle.
>
>
> On 2/8/16 5:58 PM, Ji Won Bang wrote:
>
> Dear. Freesurfer team.
>
> As another attempt, I run the motion correction without the argument
> -targrun:
>
> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
>
> However, I get the same error message again.
>
> Why is that?
>
> Thanks so much for your effort and time.
>
> I appreciate it a lot.
>
> Best,
> Ji Won
>
>
> 2016-02-08 17:16 GMT-05:00 Ji Won Bang :
>
>> Dear. Freesurfer team.
>>
>> I'd appreciate any advice from you.
>>
>> When doing the motion correction, I'd like to align all EPI
>> data(bold_retino) to the first EPI of target run(bold_decode/003). However,
>> the number of slices for target run(33) and the number of slices(32) for
>> input run(bold_retino) are different.
>>
>> When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
>> -targrun $DATA_DIR/$SUBJECT/bold_decode/003
>>
>> Freesurfer says that:
>> ** FATAL ERROR: perhaps you could make your datasets match?
>> ERROR: 3dvolreg
>> Invalid null command.
>>
>> These two kinds of run (bold_decode, bold_retino) were collected in one
>> scan per subject, so the head position should not be too different...
>>
>> Do you have any suggestions for fixing this error?
>>
>> Should I do 3dWarp -deoblique?
>>
>> Thank you so much.
>>
>> Best,
>> Ji Won
>>
>> 2016-02-08 16:30 GMT-05:00 Ji Won Bang < 
>> kirsten...@gmail.com>:
>>
>>> Dear. Freesurfer team.
>>>
>>> Hi.
>>>
>>> I'm using freesurfer 4.5 version.
>>>
>>> While doing the motion correction, an error occurred.
>>>
>>> the command I used:
>>> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun
>>> $DATA_DIR/$SUBJECT/bold_decode/003
>>>
>>> the error I have:
>>> /home/jbang/Projects/replay/epi/replay01/bold_retino
>>> 3dvolreg -verbose -dfile 025/fmc.mcdat -base
>>> 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix
>>> 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz
>>> ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit]
>>> ++ Authored by: RW Cox
>>> *+ WARNING:   If you are performing spatial transformations on an
>>> oblique dset,
>>>   such as 025/tmp.mc-afni2.32291/tempvol.nii.gz,
>>>   or viewing/combining it with volumes of differing obliquity,
>>>   you should consider running:
>>>  3dWarp -deoblique
>>>   on this and  other oblique datasets in the same session.
>>>  See 3dWarp -help for details.
>>> ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868
>>> degrees from plumb.
>>> ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz
>>> ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286
>>> degrees from plumb.
>>> ++ centers of base and input datasets are 9.09 mm apart
>>> ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD
>>> don't have same dimensions!
>>>Input: nx=74  ny=74  nz=32
>>>Base:  nx=74  ny=74  nz=33
>>> ** FATAL ERROR: perhaps you could make your datasets match?
>>> ERROR: 3dvolreg
>>> Invalid null command.
>>>
>>> I think it's because the volume size is different.

Re: [Freesurfer] Permission denied error with mri_surfcluster command

[Douglas N Greve]

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

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

Re: [Freesurfer] pial edits in subject with severe atrophy

[Corinna Bauer]

I should mention that the aseg file captures the GM outside the pial
surface.

On Wed, Feb 10, 2016 at 1:23 PM, Corinna Bauer  wrote:

> Thanks, Bruce.
> In an earlier thread from '09 with a similar problem (
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html),
> it was mentioned that there was a method being developed to edit the
> surface mesh. Is that option still available and would it help? Since this
> step in our analysis stream is central to everything else, we are willing
> to try whatever it takes.
>
> Corinna
>
> On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl  > wrote:
>
>> Sorry Corinna
>>
>> I meant to answer this the first time but it slipped through the cracks.
>> I doubt there is much you can do if there is that big a lesion. If the
>> topology is wrong and you can't see tissue in those regions it's going to
>> be very hard
>> Bruce
>>
>>
>> On Wed, 10 Feb 2016,
>> Corinna Bauer wrote:
>>
>> > Dear Experts,
>> >
>> > I have a subject with severe atrophy in bilateral frontal and parietal
>> > regions and after many rounds of edits to the brainmask, wm.mgz, and
>> control
>> > points, these regions are still left uncaptured. Is there a way to edit
>> the
>> > pial surface to include these grey matter regions? I am hesitant to draw
>> > them in via the wm surface since there is no definite WM present.
>> >
>> > I do have a FLAIR also on this subject.
>> >
>> > I've attached a couple examples.
>> >
>> > Thanks!
>> >
>> > Corinna
>> >
>> >
>> ___
>> 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.
>>
>>
>
___
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] error in motion correction

[Douglas N Greve]

I'm not sure what you are trying to do in the long run. If you have two 
different scan days and you want to test for differences between them, 
then analyze each day separately in FSFAST (no problem about the 
different number of slices). Within a day, each run is separately 
registered to the anatomical, so there is no issue about aligning to the 
first time point of the first run. Each run is aligned to the middle 
time point of each run.


On 02/10/2016 12:48 PM, Ji Won Bang wrote:
> Dear. Freesurfer team.
>
> Thanks so much your help and advice.
>
> Based on the comments, I'm trying freesurfer version 5.3.0 instead of 
> 4.5.0 now.
>
> In our experiment, each participant is scanned twice on different days 
> and the functional scan's brain volume are different (some scans have 
> 33 number of slices, some have 32 number of slices).
>
> Since participants moved a bit between scans on the same day, and the 
> head position is different between different days, my advisor advised 
> me to do co-registration between different functional scans and then 
> do co-registration between anatomical and functional scans.
>
> My question is this.
>
> If I do motion-correction such that we align all EPI data to the first 
> EPI of the first functional scan, will it be enough for 
> co-registration between different functional scans and different days? 
> Or should I do coregistration-specific process such as 
> mri_robust_register, mri_robust_template etc?

>
> Or I guess the method I choose should depend on how much the 
> participant moved between scans and how much different the head 
> position was between different days? For example, if the participant 
> was very still between runs and the head position was not that too 
> different, this motion correction is enough for coregistration between 
> functional scans. However, if not, I should do coregistration-specific 
> process such as mri_robust_register, mri_robust_template etc?
>
> I'd appreciate any of your advice.
>
> Please feel free to let me know your thoughts.
>
> Best,
> Ji Won
>
> 2016-02-08 22:31 GMT-05:00 Douglas Greve  >:
>
> In 4.5 I don't think there is a way to run it when different runs
> have different number of slices. Version 5+ will handle it
> properly. If you really want to use 4.5, then you'll have to put
> it in a different functional subdir (FSD, eg, bold), and create a
> new analysis for it, then combine them together after analysis. A
> bit of a hassle.
>
>
> On 2/8/16 5:58 PM, Ji Won Bang wrote:
>> Dear. Freesurfer team.
>>
>> As another attempt, I run the motion correction without the
>> argument -targrun:
>>
>> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
>>
>> However, I get the same error message again.
>>
>> Why is that?
>>
>> Thanks so much for your effort and time.
>>
>> I appreciate it a lot.
>>
>> Best,
>> Ji Won
>>
>>
>> 2016-02-08 17:16 GMT-05:00 Ji Won Bang > >:
>>
>> Dear. Freesurfer team.
>>
>> I'd appreciate any advice from you.
>>
>> When doing the motion correction, I'd like to align all EPI
>> data(bold_retino) to the first EPI of target
>> run(bold_decode/003). However, the number of slices for
>> target run(33) and the number of slices(32) for input
>> run(bold_retino) are different.
>>
>> When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd
>> bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003
>>
>> Freesurfer says that:
>> ** FATAL ERROR: perhaps you could make your datasets match?
>> ERROR: 3dvolreg
>> Invalid null command.
>>
>> These two kinds of run (bold_decode, bold_retino) were
>> collected in one scan per subject, so the head position
>> should not be too different...
>>
>> Do you have any suggestions for fixing this error?
>>
>> Should I do 3dWarp -deoblique?
>>
>> Thank you so much.
>>
>> Best,
>> Ji Won
>>
>> 2016-02-08 16:30 GMT-05:00 Ji Won Bang > >:
>>
>> Dear. Freesurfer team.
>>
>> Hi.
>>
>> I'm using freesurfer 4.5 version.
>>
>> While doing the motion correction, an error occurred.
>>
>> the command I used:
>> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
>> -targrun $DATA_DIR/$SUBJECT/bold_decode/003
>>
>> the error I have:
>> /home/jbang/Projects/replay/epi/replay01/bold_retino
>> 3dvolreg -verbose -dfile 025/fmc.mcdat -base
>> 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix
>> 025/tmp.mc-afni2.32291/outvol.nii.gz
>> 025/tmp.mc-afni2.32291/invol.nii.gz
>> ++ 3dvolreg: AFNI 

[Freesurfer] comparing multiple runs on the same scan

[Krieger, Donald N.]

We would like to confirm that we are getting identical results from multiple 
freesurfer runs on the same data set.
To do so we are comparing identically named files using md5sum and would very 
much appreciate your thoughts on our results.  For multiple files, we 
concatenate them and pipe the output into md5sum.  Below is a table showing 
what we've found so far.  I take hope from the positive matches we get from all 
of the .annot files and from the fact that 001.mgz does not match.  This latter 
suggests that there is a date or something embedded in some of the files from 
separate runs which defeats the match.

Please let us know what you know about this and thanks.

file(s)

md5sum result

label/*.annot

match

label/*.label

match

mri/wmparc.mgz

mismatch

surf/qsphere.nofix
surf/rh.sphere

mismatch

mri/orig/001.mgz

mismatch

mri/transforms/talairach.m3z

match

mri/transforms/talairach.m3z.inv.x.mgz
mri/transforms/talairach.m3z.inv.y.mgz
mri/transforms/talairach.m3z.inv.z.mgz

mismatch
mismatch
mismatch


Best - Don


Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh
___
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.

[Freesurfer] Permission denied error with mri_surfcluster command

[Jennifer Legault]

Dear experts,

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

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

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

This is the command I am trying to run:

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


Here is the error log:

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

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

Permission denied




Thank you for taking the time to read this email.

Sincerely,

Jennifer Legault

-- 
Jennifer Legault
Ph.D candidate, Neuroscience
Brain, Language, and Computation Lab
The Pennsylvania State University
___
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

[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] error in motion correction

[Douglas N Greve]

This is the right way to do it, but it may be over kill. I doubt the 
fMRI results are going to change much whether you use the anatomical 
from first day only, the 2nd day only, or a combination of the two.


On 02/10/2016 01:25 PM, Martin Reuter wrote:
> Hi,
>
> you should co register your structural scans with robust-register or 
> robust-template (if you have more than 2). This can be done into the 
> midspace to make sure both time points are mapped to avoid processing 
> bias.
>
> You can then register the functional scans to their corresponding 
> structurals and concat the transforms to get everything into the same 
> midspace.
>
> Best, Martin
>
>
> On 02/10/2016 12:48 PM, Ji Won Bang wrote:
>> Dear. Freesurfer team.
>>
>> Thanks so much your help and advice.
>>
>> Based on the comments, I'm trying freesurfer version 5.3.0 instead of 
>> 4.5.0 now.
>>
>> In our experiment, each participant is scanned twice on different 
>> days and the functional scan's brain volume are different (some scans 
>> have 33 number of slices, some have 32 number of slices).
>>
>> Since participants moved a bit between scans on the same day, and the 
>> head position is different between different days, my advisor advised 
>> me to do co-registration between different functional scans and then 
>> do co-registration between anatomical and functional scans.
>>
>> My question is this.
>>
>> If I do motion-correction such that we align all EPI data to the 
>> first EPI of the first functional scan, will it be enough for 
>> co-registration between different functional scans and different 
>> days? Or should I do coregistration-specific process such as 
>> mri_robust_register, mri_robust_template etc?
>>
>> Or I guess the method I choose should depend on how much the 
>> participant moved between scans and how much different the head 
>> position was between different days? For example, if the participant 
>> was very still between runs and the head position was not that too 
>> different, this motion correction is enough for coregistration 
>> between functional scans. However, if not, I should do 
>> coregistration-specific process such as mri_robust_register, 
>> mri_robust_template etc?
>>
>> I'd appreciate any of your advice.
>>
>> Please feel free to let me know your thoughts.
>>
>> Best,
>> Ji Won
>>
>> 2016-02-08 22:31 GMT-05:00 Douglas Greve > >:
>>
>> In 4.5 I don't think there is a way to run it when different runs
>> have different number of slices. Version 5+ will handle it
>> properly. If you really want to use 4.5, then you'll have to put
>> it in a different functional subdir (FSD, eg, bold), and create a
>> new analysis for it, then combine them together after analysis. A
>> bit of a hassle.
>>
>>
>> On 2/8/16 5:58 PM, Ji Won Bang wrote:
>>> Dear. Freesurfer team.
>>>
>>> As another attempt, I run the motion correction without the
>>> argument -targrun:
>>>
>>> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
>>>
>>> However, I get the same error message again.
>>>
>>> Why is that?
>>>
>>> Thanks so much for your effort and time.
>>>
>>> I appreciate it a lot.
>>>
>>> Best,
>>> Ji Won
>>>
>>>
>>> 2016-02-08 17:16 GMT-05:00 Ji Won Bang :
>>>
>>> Dear. Freesurfer team.
>>>
>>> I'd appreciate any advice from you.
>>>
>>> When doing the motion correction, I'd like to align all EPI
>>> data(bold_retino) to the first EPI of target
>>> run(bold_decode/003). However, the number of slices for
>>> target run(33) and the number of slices(32) for input
>>> run(bold_retino) are different.
>>>
>>> When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd
>>> bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003
>>>
>>> Freesurfer says that:
>>> ** FATAL ERROR: perhaps you could make your datasets match?
>>> ERROR: 3dvolreg
>>> Invalid null command.
>>>
>>> These two kinds of run (bold_decode, bold_retino) were
>>> collected in one scan per subject, so the head position
>>> should not be too different...
>>>
>>> Do you have any suggestions for fixing this error?
>>>
>>> Should I do 3dWarp -deoblique?
>>>
>>> Thank you so much.
>>>
>>> Best,
>>> Ji Won
>>>
>>> 2016-02-08 16:30 GMT-05:00 Ji Won Bang :
>>>
>>> Dear. Freesurfer team.
>>>
>>> Hi.
>>>
>>> I'm using freesurfer 4.5 version.
>>>
>>> While doing the motion correction, an error occurred.
>>>
>>> the command I used:
>>> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino
>>> -targrun $DATA_DIR/$SUBJECT/bold_decode/003
>>>
>>> the error I have:
>>> /home/jbang/Projects/replay/epi/replay01/bold_retino
>>>  

Re: [Freesurfer] pial edits in subject with severe atrophy

[Corinna Bauer]

ok thanks.

On Wed, Feb 10, 2016 at 3:40 PM, Bruce Fischl 
wrote:

> not to my knowledge, but others may have developed something
> Bruce
> On Wed, 10 Feb
> 2016, Corinna Bauer wrote:
>
> > Thanks, Bruce.
> > In an earlier thread from '09 with a similar problem(
> https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html
> > ), it was mentioned that there was a method being developed to edit the
> > surface mesh. Is that option still available and would it help? Since
> this
> > step in our analysis stream is central to everything else, we are
> willing to
> > try whatever it takes.
> >
> > Corinna
> >
> > On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > wrote:
> >   Sorry Corinna
> >
> >   I meant to answer this the first time but it slipped through the
> >   cracks.
> >   I doubt there is much you can do if there is that big a lesion.
> >   If the
> >   topology is wrong and you can't see tissue in those regions it's
> >   going to
> >   be very hard
> >   Bruce
> >
> >
> >   On Wed, 10 Feb 2016,
> >   Corinna Bauer wrote:
> >
> >   > Dear Experts,
> >   >
> >   > I have a subject with severe atrophy in bilateral frontal and
> >   parietal
> >   > regions and after many rounds of edits to the brainmask,
> >   wm.mgz, and control
> >   > points, these regions are still left uncaptured. Is there a
> >   way to edit the
> >   > pial surface to include these grey matter regions? I am
> >   hesitant to draw
> >   > them in via the wm surface since there is no definite WM
> >   present.
> >   >
> >   > I do have a FLAIR also on this subject.
> >   >
> >   > I've attached a couple examples.
> >   >
> >   > Thanks!
> >   >
> >   > Corinna
> >   >
> >   >
> > ___
> > 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.
> >
> >
> >
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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

Re: [Freesurfer] To use a ROI.label as seed in FS-FAST

[stdp82]

If I use:
mri_label2vol --label ramgseed_rhsurf.label --temp 
$SUBJECTS_DIR/subj/mri/orig.mgz --identity --subject fsaverage --hemi rh --o 
RIGHT_ROI.nii.gz --fill-ribbon
ERROR: Option --fill-ribbon unknown



Messaggio originale

Da: std...@virgilio.it

Data: 8-feb-2016 20.35

A: "Freesurfer support list"

Ogg: [Freesurfer] R: Re:  To use a ROI.label as seed in FS-FAST



Thanks.I have down a right ad left ROI on the surface.Next, I have run:
mri_label2vol --label ramgseed_rhsurf.label --temp 
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh 
--o RIGHT_ROI.nii.gzmri_label2vol --label ramgseed_lhsurf.label --temp 
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject fsaverage --hemi rh 
--o LEFT_ROI.nii.gz

mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgzmri_convert LEFT_ROI.nii.gz 
LEFT_ROI.mgz

fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg 
RIGHT_ROI.configfcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg 
LEFT_ROI.config

fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config
fcseed-sess -s subj1_FS -cfg LEFT_ROI.config
but during fcseed-sess this error occurs:
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $cwd cmdline 
mri_segstats --i 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz --seg 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz
 --id 1 --sum 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum
 --avgwfvol 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh
 sysname  Darwinhostname iMac-di-Stefano.localmachine  x86_64user 
StefanoUseRobust  0Loading 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gzLoading
 /Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gzVoxel Volume 
is 64.5752 mm^3Generating list of segmentation idsFound   1 
segmentationsComputing statistics for each segmentation  0 1
  0   0.000MRIalloc(0, 1, 1): bad parmReporting on  
 0 segmentationsComputing spatial average of each frameWriting to 
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mghSegmentation
 fault 



Messaggio originale

Da: Douglas Greve 

Data: 8-feb-2016 4.38

A: 

Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST




  
  
Use mri_label2vol to convert the label into a volume in the
anatomical space and store it in $SUBJECTS_DIR/subject/mri. Make
sure to use --fill-ribbon if the label is surface-based. When
running fcseed-config, specify the volume with the -seg option and
use -segid 1



On 2/7/16 3:16 PM, std...@virgilio.it
  wrote:



  Hi list,




I would like to use as seed in FS-FAST a ROI.label which I
  have drawn on a cluster in tksurfer.
How can I do it?
Should I use mri_label2vol?


  
Thanks.



Stefano


  
  

  

  
  

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



  













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


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

Re: [Freesurfer] comparing multiple runs on the same scan

[dgw]

Doug responded to your previous mail with this:

Even on the same operating system they will be different because there
is stuff in the header that will change. Use mri_diff (volumes,
segmentations, and surface overlays) or mris_diff for surfaces to check
whether they are different.


hth
d


On Wed, Feb 10, 2016 at 2:14 PM, Krieger, Donald N. 
wrote:

> We would like to confirm that we are getting identical results from
> multiple freesurfer runs on the same data set.
>
> To do so we are comparing identically named files using md5sum and would
> very much appreciate your thoughts on our results.  For multiple files, we
> concatenate them and pipe the output into md5sum.  Below is a table showing
> what we’ve found so far.  I take hope from the positive matches we get from
> all of the .annot files and from the fact that 001.mgz does not match.
> This latter suggests that there is a date or something embedded in some of
> the files from separate runs which defeats the match.
>
>
>
> Please let us know what you know about this and thanks.
>
>
>
> file(s)
>
> md5sum result
>
> label/*.annot
>
> match
>
> label/*.label
>
> match
>
> mri/wmparc.mgz
>
> mismatch
>
> surf/qsphere.nofix
>
> surf/rh.sphere
>
> mismatch
>
> mri/orig/001.mgz
>
> mismatch
>
> mri/transforms/talairach.m3z
>
> match
>
> mri/transforms/talairach.m3z.inv.x.mgz
>
> mri/transforms/talairach.m3z.inv.y.mgz
>
> mri/transforms/talairach.m3z.inv.z.mgz
>
> mismatch
>
> mismatch
>
> mismatch
>
>
>
> Best - Don
>
>
>
>
>
> Don Krieger, Ph.D.
>
> Department of Neurological Surgery
>
> University of Pittsburgh
>
> ___
> 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.
>
>
___
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] comparing multiple runs on the same scan

[Krieger, Donald N.]

Thanks very much for getting back so quickly.
Please pardon.
I’m sure this answer must be in lots of other places.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of dgw
Sent: Wednesday, February 10, 2016 3:17 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] comparing multiple runs on the same scan

Doug responded to your previous mail with this:

Even on the same operating system they will be different because there
is stuff in the header that will change. Use mri_diff (volumes,
segmentations, and surface overlays) or mris_diff for surfaces to check
whether they are different.
[Image removed by sender.]
hth
d


On Wed, Feb 10, 2016 at 2:14 PM, Krieger, Donald N. 
> wrote:
We would like to confirm that we are getting identical results from multiple 
freesurfer runs on the same data set.
To do so we are comparing identically named files using md5sum and would very 
much appreciate your thoughts on our results.  For multiple files, we 
concatenate them and pipe the output into md5sum.  Below is a table showing 
what we’ve found so far.  I take hope from the positive matches we get from all 
of the .annot files and from the fact that 001.mgz does not match.  This latter 
suggests that there is a date or something embedded in some of the files from 
separate runs which defeats the match.

Please let us know what you know about this and thanks.

file(s)

md5sum result

label/*.annot

match

label/*.label

match

mri/wmparc.mgz

mismatch

surf/qsphere.nofix
surf/rh.sphere

mismatch

mri/orig/001.mgz

mismatch

mri/transforms/talairach.m3z

match

mri/transforms/talairach.m3z.inv.x.mgz
mri/transforms/talairach.m3z.inv.y.mgz
mri/transforms/talairach.m3z.inv.z.mgz

mismatch
mismatch
mismatch


Best - Don


Don Krieger, Ph.D.
Department of Neurological Surgery
University of Pittsburgh

___
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.

___
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] pial edits in subject with severe atrophy

[Bruce Fischl]

not to my knowledge, but others may have developed something
Bruce
On Wed, 10 Feb 
2016, Corinna Bauer wrote:

> Thanks, Bruce.
> In an earlier thread from '09 with a similar 
> problem(https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html
> ), it was mentioned that there was a method being developed to edit the
> surface mesh. Is that option still available and would it help? Since this
> step in our analysis stream is central to everything else, we are willing to
> try whatever it takes.
> 
> Corinna
> 
> On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl 
> wrote:
>   Sorry Corinna
>
>   I meant to answer this the first time but it slipped through the
>   cracks.
>   I doubt there is much you can do if there is that big a lesion.
>   If the
>   topology is wrong and you can't see tissue in those regions it's
>   going to
>   be very hard
>   Bruce
> 
>
>   On Wed, 10 Feb 2016,
>   Corinna Bauer wrote:
>
>   > Dear Experts,
>   >
>   > I have a subject with severe atrophy in bilateral frontal and
>   parietal
>   > regions and after many rounds of edits to the brainmask,
>   wm.mgz, and control
>   > points, these regions are still left uncaptured. Is there a
>   way to edit the
>   > pial surface to include these grey matter regions? I am
>   hesitant to draw
>   > them in via the wm surface since there is no definite WM
>   present.
>   >
>   > I do have a FLAIR also on this subject.
>   >
>   > I've attached a couple examples.
>   >
>   > Thanks!
>   >
>   > Corinna
>   >
>   >
> ___
> 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.
> 
> 
> 
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] comparing multiple runs on the same scan

[Bruce Fischl]

Hi Don

are you saying the 001.mgz is different when created from the same dicom 
data? Can you run mri_diff on it to see what the difference is?


cheers
Bruce
On Wed, 10 
Feb 2016, Krieger, Donald N. wrote:




We would like to confirm that we are getting identical results from multiple
freesurfer runs on the same data set.

To do so we are comparing identically named files using md5sum and would
very much appreciate your thoughts on our results.  For multiple files, we
concatenate them and pipe the output into md5sum.  Below is a table showing
what we’ve found so far.  I take hope from the positive matches we get from
all of the .annot files and from the fact that 001.mgz does not match.  This
latter suggests that there is a date or something embedded in some of the
files from separate runs which defeats the match.

 

Please let us know what you know about this and thanks.

 

file(s)

md5sum result

label/*.annot

match

label/*.label

match

mri/wmparc.mgz

mismatch

surf/qsphere.nofix

surf/rh.sphere

mismatch

mri/orig/001.mgz

mismatch

mri/transforms/talairach.m3z

match

mri/transforms/talairach.m3z.inv.x.mgz

mri/transforms/talairach.m3z.inv.y.mgz

mri/transforms/talairach.m3z.inv.z.mgz

mismatch

mismatch

mismatch

 

Best - Don

 

 

Don Krieger, Ph.D.

Department of Neurological Surgery

University of Pittsburgh


___
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] comparing multiple runs on the same scan

[Krieger, Donald N.]

mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are 
different.
In fact, their sizes are slightly different.



> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, February 10, 2016 3:45 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> 
> Hi Don
> 
> are you saying the 001.mgz is different when created from the same dicom
> data? Can you run mri_diff on it to see what the difference is?
> 
> cheers
> Bruce
> On Wed, 10
> Feb 2016, Krieger, Donald N. wrote:
> 
> >
> > We would like to confirm that we are getting identical results from
> > multiple freesurfer runs on the same data set.
> >
> > To do so we are comparing identically named files using md5sum and
> > would very much appreciate your thoughts on our results.  For multiple
> > files, we concatenate them and pipe the output into md5sum.  Below is
> > a table showing what we’ve found so far.  I take hope from the
> > positive matches we get from all of the .annot files and from the fact
> > that 001.mgz does not match.  This latter suggests that there is a
> > date or something embedded in some of the files from separate runs which
> defeats the match.
> >
> >
> >
> > Please let us know what you know about this and thanks.
> >
> >
> >
> > file(s)
> >
> > md5sum result
> >
> > label/*.annot
> >
> > match
> >
> > label/*.label
> >
> > match
> >
> > mri/wmparc.mgz
> >
> > mismatch
> >
> > surf/qsphere.nofix
> >
> > surf/rh.sphere
> >
> > mismatch
> >
> > mri/orig/001.mgz
> >
> > mismatch
> >
> > mri/transforms/talairach.m3z
> >
> > match
> >
> > mri/transforms/talairach.m3z.inv.x.mgz
> >
> > mri/transforms/talairach.m3z.inv.y.mgz
> >
> > mri/transforms/talairach.m3z.inv.z.mgz
> >
> > mismatch
> >
> > mismatch
> >
> > mismatch
> >
> >
> >
> > Best - Don
> >
> >
> >
> >
> >
> > Don Krieger, Ph.D.
> >
> > Department of Neurological Surgery
> >
> > University of Pittsburgh
> >
> >
> >

___
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

[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] comparing multiple runs on the same scan

[Bruce Fischl]

what is the difference in how you created them?
On Wed, 10 Feb 2016, 
Krieger, Donald N. wrote:



mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are 
different.
In fact, their sizes are slightly different.




-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, February 10, 2016 3:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] comparing multiple runs on the same scan

Hi Don

are you saying the 001.mgz is different when created from the same dicom
data? Can you run mri_diff on it to see what the difference is?

cheers
Bruce
On Wed, 10
Feb 2016, Krieger, Donald N. wrote:



We would like to confirm that we are getting identical results from
multiple freesurfer runs on the same data set.

To do so we are comparing identically named files using md5sum and
would very much appreciate your thoughts on our results.  For multiple
files, we concatenate them and pipe the output into md5sum.  Below is
a table showing what we’ve found so far.  I take hope from the
positive matches we get from all of the .annot files and from the fact
that 001.mgz does not match.  This latter suggests that there is a
date or something embedded in some of the files from separate runs which

defeats the match.




Please let us know what you know about this and thanks.



file(s)

md5sum result

label/*.annot

match

label/*.label

match

mri/wmparc.mgz

mismatch

surf/qsphere.nofix

surf/rh.sphere

mismatch

mri/orig/001.mgz

mismatch

mri/transforms/talairach.m3z

match

mri/transforms/talairach.m3z.inv.x.mgz

mri/transforms/talairach.m3z.inv.y.mgz

mri/transforms/talairach.m3z.inv.z.mgz

mismatch

mismatch

mismatch



Best - Don





Don Krieger, Ph.D.

Department of Neurological Surgery

University of Pittsburgh





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


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


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

Re: [Freesurfer] Middle cerebellar peduncle segmentation

[Eugenio Iglesias]

Dear Henri, 
As of today, there's no plan to add any new labels to the brainstem atlas. 
Cheers, 
/Eugenio 

Juan Eugenio Iglesias 
Postdoctoral researcher BCBL 
www.jeiglesias.com 
www.bcbl.eu 

Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer 


From: "Henri Pazro"  
To: "Freesurfer support list"  
Sent: Wednesday, February 10, 2016 6:27:47 PM 
Subject: [Freesurfer] Middle cerebellar peduncle segmentation 

Dear experts, 

I'm trying the brainstem segmentation from Juan Eugenio Iglesias and would like 
to know if the middle cerebellar peduncle will be added in a near future? 

Thanks! 

H. 

___ 
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. 
___
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] pial edits in subject with severe atrophy

[Corinna Bauer]

Thanks, Bruce.
In an earlier thread from '09 with a similar problem (
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-May/010554.html),
it was mentioned that there was a method being developed to edit the
surface mesh. Is that option still available and would it help? Since this
step in our analysis stream is central to everything else, we are willing
to try whatever it takes.

Corinna

On Wed, Feb 10, 2016 at 12:19 PM, Bruce Fischl 
wrote:

> Sorry Corinna
>
> I meant to answer this the first time but it slipped through the cracks.
> I doubt there is much you can do if there is that big a lesion. If the
> topology is wrong and you can't see tissue in those regions it's going to
> be very hard
> Bruce
>
>
> On Wed, 10 Feb 2016,
> Corinna Bauer wrote:
>
> > Dear Experts,
> >
> > I have a subject with severe atrophy in bilateral frontal and parietal
> > regions and after many rounds of edits to the brainmask, wm.mgz, and
> control
> > points, these regions are still left uncaptured. Is there a way to edit
> the
> > pial surface to include these grey matter regions? I am hesitant to draw
> > them in via the wm surface since there is no definite WM present.
> >
> > I do have a FLAIR also on this subject.
> >
> > I've attached a couple examples.
> >
> > Thanks!
> >
> > Corinna
> >
> >
> ___
> 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.
>
>
___
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

[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.

[Freesurfer] difference in 001.mgz found

[Krieger, Donald N.]

These runs were executed on the Open Science Grid.
So the data file, the scan, was uploaded to grid worker machine, placed in a 
transitory directory, and processed.
The full pathname of the file is included in 001.mgz.
I got it by: zcat mri/orig/001.mgz | strings
Here are the input and output file names for 2 of the runs:
/var/lib/condor/execute/dir_31034/MRN_1_defaced.mgz 
/scratch/tmp.FFTGBhmgp8/MRN_1/mri/orig/001.mgz

/var/lib/condor/execute/dir_3734674/glide_HRFaAm/execute/dir_3741395/MRN_1_defaced.mgz
 /scratch/tmp.ghJfB4leGR/MRN_1/mri/orig/001.mgz

Best - Don


> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Krieger, Donald N.
> Sent: Wednesday, February 10, 2016 6:38 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> 
> It looks like they do give the same results.
> I have to write something to go through everything systematically which I may
> not get to till tomorrow.
> Also I am checking to see whether there was some difference in how 001.mgz
> was created.
> The source image file on which we are running freesurfer is a defaced.mgz .
> It's possible that it was sitting in a different directory for the different 
> runs
> since the runs were executed by a work flow management system (Pegasus) on
> the Open Science Grid.
> 
> Don
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-
> boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, February 10, 2016 6:13 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> 
> That probably means that there is something in the header that is different. 
> It
> should print a report to the terminal. Do they not give the same results?
> 
> On 02/10/2016 04:36 PM, Krieger, Donald N. wrote:
> > mri_diff finds no differences in the mri/orig/001.mgz's but the checksums 
> > are
> different.
> > In fact, their sizes are slightly different.
> >
> >
> >
> >> -Original Message-
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> >> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> >> Sent: Wednesday, February 10, 2016 3:45 PM
> >> To: Freesurfer support list
> >> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> >>
> >> Hi Don
> >>
> >> are you saying the 001.mgz is different when created from the same
> >> dicom data? Can you run mri_diff on it to see what the difference is?
> >>
> >> cheers
> >> Bruce
> >> On Wed, 10
> >> Feb 2016, Krieger, Donald N. wrote:
> >>
> >>> We would like to confirm that we are getting identical results from
> >>> multiple freesurfer runs on the same data set.
> >>>
> >>> To do so we are comparing identically named files using md5sum and
> >>> would very much appreciate your thoughts on our results.  For
> >>> multiple files, we concatenate them and pipe the output into md5sum.
> >>> Below is a table showing what we’ve found so far.  I take hope from
> >>> the positive matches we get from all of the .annot files and from
> >>> the fact that 001.mgz does not match.  This latter suggests that
> >>> there is a date or something embedded in some of the files from
> >>> separate runs which
> >> defeats the match.
> >>>
> >>>
> >>> Please let us know what you know about this and thanks.
> >>>
> >>>
> >>>
> >>> file(s)
> >>>
> >>> md5sum result
> >>>
> >>> label/*.annot
> >>>
> >>> match
> >>>
> >>> label/*.label
> >>>
> >>> match
> >>>
> >>> mri/wmparc.mgz
> >>>
> >>> mismatch
> >>>
> >>> surf/qsphere.nofix
> >>>
> >>> surf/rh.sphere
> >>>
> >>> mismatch
> >>>
> >>> mri/orig/001.mgz
> >>>
> >>> mismatch
> >>>
> >>> mri/transforms/talairach.m3z
> >>>
> >>> match
> >>>
> >>> mri/transforms/talairach.m3z.inv.x.mgz
> >>>
> >>> mri/transforms/talairach.m3z.inv.y.mgz
> >>>
> >>> mri/transforms/talairach.m3z.inv.z.mgz
> >>>
> >>> mismatch
> >>>
> >>> mismatch
> >>>
> >>> mismatch
> >>>
> >>>
> >>>
> >>> Best - Don
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> Don Krieger, Ph.D.
> >>>
> >>> Department of Neurological Surgery
> >>>
> >>> University of Pittsburgh
> >>>
> >>>
> >>>
> > ___
> > 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
> 
> 
> 

Re: [Freesurfer] epidewarp.fsl for FSL 5.x

[Douglas Greve]

what is your command line? I think there is a rescaling in which it 
expcts the phase to be 0-2048 (or 4096) as this is how it comes of the 
(siemens) scanner. Could that be the problem?



On 2/10/16 10:40 PM, Joseph Dien wrote:

I ran into the same issue:

FSLVersion 5.0.4
FSLVerMaj 5
FSL Version is 5.0.4, must be 3.X or 4.X

I downloaded the epidewarp.fsl script from the suggested ftp site and 
replaced the existing script.  It did indeed fix the version 
incompatibility with FSL 5.x.


I ran into a new problem where it was aborting.  After some trouble 
shooting and looking over the documentation, I realized that —-epi is 
a required input without which the script crashes (or is it supposed 
to be optional but there is a bug in the script?).


After including it, it ran much further but then aborted with the 
following error:


ERROR: input phase image exceeds allowable phase range.
Allowable range is 6.283 radians.  Image range is: 12.5633 radians.

This is consistent with the documentation.  I’m not sure why the phase 
image exceeds the range though.


It ran without problems with SPM’s FieldMap Toolbox and it is from a 
standard Siemen’s scanner sequence (two magnitude files and one phase 
difference file).


Do I just divide the values by two with something like fslmaths since 
it seems to have exactly double the required range?


Joe

On Nov 26, 2014, at 21:36, Douglas Greve > wrote:



It is there again. I don't know what the status if it  is in terms of 
the version. Try it and let me know

doug

On 11/25/14 4:34 PM, Morgan Hough wrote:

Hi Doug,

Could you put the epidewarp.fsl script back on your ftp site? I 
don’t see it at the link in the archives:


ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl

BTW, is the script updated in some way for 5.x or can I can the old 
script just be changed to accept 5.x version numbers.


Cheers,

-Morgan


___
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.




Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com 
Cell Phone: 202-297-8117
http://joedien.com



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


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


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

Re: [Freesurfer] Processing of young children using Freesurfer

[Zoellner, Frank]

Hi,

did you find a hint why my installation of freesurfer is not processing the 
data at that stage ?
It seems to be a general problem, we tried also with other data sets of elder 
people etc ..

Any help appreciated.

Yours
Frank


PD Dr. Frank Zoellner
Group Leader "MRI and Medical Image Analysis" 
Computer Assisted Clinical Medicine
Medical Faculty Mannheim
Heidelberg University
Theodor-Kutzer-Ufer 1-3
D-68167 Mannheim

Phone: +49 (0)621 3835117
Fax:   +49 (0)621 3835123
Email: frank.zoell...@medma.uni-heidelberg.de 
Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/


-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Zoellner, Frank
Gesendet: Dienstag, 9. Februar 2016 15:49
An: Freesurfer support list
Betreff: Re: [Freesurfer] Processing of young children using Freesurfer

Hi Bruce,

thanks for the reply.
 Here comes the output (see attached).

I just downloaded the VM with freesurfer from your website, fyi.

Yours
Frank

PD Dr. Frank Zoellner
Group Leader "MRI and Medical Image Analysis" 
Computer Assisted Clinical Medicine
Medical Faculty Mannheim
Heidelberg University
Theodor-Kutzer-Ufer 1-3
D-68167 Mannheim

Phone: +49 (0)621 3835117
Fax:   +49 (0)621 3835123
Email: frank.zoell...@medma.uni-heidelberg.de 
Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/


-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Bruce Fischl
Gesendet: Dienstag, 9. Februar 2016 14:12
An: Freesurfer support list
Betreff: Re: [Freesurfer] Processing of young children using Freesurfer

hmmm, this doesn't seem to have to do with your data but maybe is an 
installation problem? It says it failed but doesn't give an error message, 
which is unusual. Can you try just typing in directly:

cd /media/sf_cdh_ventrikel/test_002/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i 
orig.mgz --o orig_nu.mgz

and send us the output?

cheers
Bruce

On Tue, 9
Feb 2016, Zoellner, Frank wrote:

> Hi,
>  
> I am currently working on a project involving brain morphometry of 2 
> year old children.
> We are interested in segmenting the ventricle and I tried to run 
> freesurfer using the standard recon-all  -all for a first test.
>  
> Unfortunately, freesurfer reports an error (see attached log file).
>  
> I also read about that it is advised to run freesurfer with patient 
> age >5 but maybe someone has an idea how to solve this.
> As far as I get from the step it crashes at the intensity correction step?
> Do I need to calculate some sort of template maybe ?
>  
> Any comments welcome
>  
> Yours
> Frank
>  
> 
> PD Dr. Frank Zoellner
> Group Leader "MRI and Medical Image Analysis"
> Computer Assisted Clinical Medicine
> Medical Faculty Mannheim
> Heidelberg University
> Theodor-Kutzer-Ufer 1-3
> D-68167 Mannheim
>  
> Phone: +49 (0)621 3835117
> Fax:   +49 (0)621 3835123
> Email: frank.zoell...@medma.uni-heidelberg.de
> Web: http://www.umm.uni-heidelberg.de/inst/cbtm/ckm/
>  
>  
>  
> 
>

___
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] epidewarp.fsl for FSL 5.x

[Joseph Dien]

I ran into the same issue:

FSLVersion 5.0.4
FSLVerMaj 5
FSL Version is 5.0.4, must be 3.X or 4.X

I downloaded the epidewarp.fsl script from the suggested ftp site and replaced 
the existing script.  It did indeed fix the version incompatibility with FSL 
5.x.

I ran into a new problem where it was aborting.  After some trouble shooting 
and looking over the documentation, I realized that —-epi is a required input 
without which the script crashes (or is it supposed to be optional but there is 
a bug in the script?).

After including it, it ran much further but then aborted with the following 
error:

ERROR: input phase image exceeds allowable phase range.
Allowable range is 6.283 radians.  Image range is: 12.5633 radians.

This is consistent with the documentation.  I’m not sure why the phase image 
exceeds the range though.

It ran without problems with SPM’s FieldMap Toolbox and it is from a standard 
Siemen’s scanner sequence (two magnitude files and one phase difference file).

Do I just divide the values by two with something like fslmaths since it seems 
to have exactly double the required range?

Joe

> On Nov 26, 2014, at 21:36, Douglas Greve  wrote:
> 
> 
> It is there again. I don't know what the status if it  is in terms of the 
> version. Try it and let me know
> doug
> 
> On 11/25/14 4:34 PM, Morgan Hough wrote:
>> Hi Doug,
>> 
>> Could you put the epidewarp.fsl script back on your ftp site? I don’t see it 
>> at the link in the archives:
>> 
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl 
>> 
>> 
>> BTW, is the script updated in some way for 5.x or can I can the old script 
>> just be changed to accept 5.x version numbers. 
>> 
>> Cheers,
>> 
>> -Morgan
> 
> ___
> 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.



Joseph Dien, PhD
Senior Research Scientist
Maryland Neuroimaging Center
University of Maryland, College Park
E-mail: jdie...@mac.com
Cell Phone: 202-297-8117
http://joedien.com

___
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] To use a ROI.label as seed in FS-FAST

[Douglas Greve]

 I may have gotten the exact form of the flag wrong. When it says an 
option is not known, you should try running the command with --help to 
see if something similar is there. In this way,  you might be able to 
figure it out for yourself rather than have to wait a day or so for us 
to respond.

doug



On 2/10/16 4:20 PM, std...@virgilio.it wrote:




If I use:

mri_label2vol --label ramgseed_rhsurf.label --temp
$SUBJECTS_DIR/subj/mri/orig.mgz --identity --subject fsaverage
--hemi rh --o RIGHT_ROI.nii.gz --fill-ribbon

ERROR: Option --fill-ribbon unknown


Messaggio originale
Da: std...@virgilio.it
Data: 8-feb-2016 20.35
A: "Freesurfer support list"
Ogg: [Freesurfer] R: Re: To use a ROI.label as seed in FS-FAST

Thanks.
I have down a right ad left ROI on the surface.
Next, I have run:

mri_label2vol --label ramgseed_rhsurf.label --temp
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject
fsaverage --hemi rh --o RIGHT_ROI.nii.gz
mri_label2vol --label ramgseed_lhsurf.label --temp
$SUBJECTS_DIR/fsaverage/mri/orig.mgz --identity --subject
fsaverage --hemi rh --o LEFT_ROI.nii.gz

mri_convert RIGHT_ROI.nii.gz RIGHT_ROI.mgz
mri_convert LEFT_ROI.nii.gz LEFT_ROI.mgz

fcseed-config -segid 1 -seg RIGHT_ROI.mgz -fsd rest -mean -cfg
RIGHT_ROI.config
fcseed-config -segid 1 -seg LEFT_ROI.mgz -fsd rest -mean -cfg
LEFT_ROI.config

fcseed-sess -s subj1_FS -cfg RIGHT_ROI.config
fcseed-sess -s subj1_FS -cfg LEFT_ROI.config

but during fcseed-sess this error occurs:

$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
cwd
cmdline mri_segstats --i
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz
--seg

/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz
--id 1 --sum

/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/junk.sum
--avgwfvol

/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh

sysname  Darwin
hostname iMac-di-Stefano.local
machine  x86_64
user Stefano
UseRobust  0
Loading

/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/mask.nii.gz
Loading
/Applications/freesurfer/subjects/fMRI/subj1/rest/001/fmcpr.nii.gz
Voxel Volume is 64.5752 mm^3
Generating list of segmentation ids
Found   1 segmentations
Computing statistics for each segmentation
  0 1   0   0.000
MRIalloc(0, 1, 1): bad parm

Reporting on   0 segmentations
Computing spatial average of each frame

Writing to

/Applications/freesurfer/subjects/fMRI/subj1/rest/001/tmp.fcseed-sess.55700/avgwf.mgh
Segmentation fault


Messaggio originale
Da: Douglas Greve 
Data: 8-feb-2016 4.38
A: 
Ogg: Re: [Freesurfer] To use a ROI.label as seed in FS-FAST

Use mri_label2vol to convert the label into a volume in
the anatomical space and store it in
$SUBJECTS_DIR/subject/mri. Make sure to use --fill-ribbon
if the label is surface-based. When running fcseed-config,
specify the volume with the -seg option and use -segid 1

On 2/7/16 3:16 PM, std...@virgilio.it wrote:


Hi list,

I would like to use as seed in FS-FAST a ROI.label
which I have drawn on a cluster in tksurfer.
How can I do it?
Should I use mri_label2vol?

Thanks.

Stefano




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










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


___
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

[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] abnormal inflated surface

[dgw]

Hi Jasmin,

nothing looks wrong with the inflated brain images to me. Remember,
the inflated brain doesn't have the same space as the T1 or white
matter surface, so they are just centered. And overlap one another as
the slice views showed. I'm afraid I can't help with the hippocampal
question, though you may want to try adding some details.

hth
d

On Wed, Feb 10, 2016 at 5:30 PM, Jasmin Alves  wrote:
> Hello freesurfer,
>
> I received this odd inflated surface image. I am not sure if this is
> something that can be fixed via a registration step or should be fixed in
> another step. Your input as to how to correct this image would be greatly
> appreciated. Also, I noticed that this participant's hippocampal volume is
> half the amount compared to the rest of my participants. Is it possible
> these two problems are related or am I possibly dealing with two separate
> issues? I have attached a screen shot of both problems.
>
> Thank you very much,
> Jasmin
>
> --
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu
>
>
> ___
> 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.
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] abnormal inflated surface

[Jasmin Alves]

Hello,

Thank you for the speedy reply. I ran recon-all and the process occurred
without error. I have quality checked the various steps and have found no
issues. But this participant's hippocampal volume is approximately 2000
while all the others in my cohort are about 4000. Is it possible for there
to be such a large discrepancy? The participants are all the same age. Is
this sufficient information?

Thanks again,
Jasmin

On Wed, Feb 10, 2016 at 2:37 PM, dgw  wrote:

> Hi Jasmin,
>
> nothing looks wrong with the inflated brain images to me. Remember,
> the inflated brain doesn't have the same space as the T1 or white
> matter surface, so they are just centered. And overlap one another as
> the slice views showed. I'm afraid I can't help with the hippocampal
> question, though you may want to try adding some details.
>
> hth
> d
>
> On Wed, Feb 10, 2016 at 5:30 PM, Jasmin Alves  wrote:
> > Hello freesurfer,
> >
> > I received this odd inflated surface image. I am not sure if this is
> > something that can be fixed via a registration step or should be fixed in
> > another step. Your input as to how to correct this image would be greatly
> > appreciated. Also, I noticed that this participant's hippocampal volume
> is
> > half the amount compared to the rest of my participants. Is it possible
> > these two problems are related or am I possibly dealing with two separate
> > issues? I have attached a screen shot of both problems.
> >
> > Thank you very much,
> > Jasmin
> >
> > --
> > Jasmin Alves
> > Predoctoral Student
> > Medical Biology Graduate Program
> > University of Southern California
> > jal...@usc.edu
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=CwICAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=MXAJrRl5ZThq3OG0Uf0wJo61Z-JfF3OS0ng6ViRC18s=XEgU8Fh1wGcYqmtsBazRiOZIu0gUp1SLFYlLskyZLZE=
> >
> >
> > 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
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_complianceline=CwICAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=MXAJrRl5ZThq3OG0Uf0wJo61Z-JfF3OS0ng6ViRC18s=npocjT9ClTUdB8WKhwwXLpFmrOjb1foUBjnrRLZH7nU=
> . 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.
> >
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer=CwICAg=clK7kQUTWtAVEOVIgvi0NU5BOUHhpN0H8p7CSfnc_gI=LH_W279i0KTyqa6rNRHLug=MXAJrRl5ZThq3OG0Uf0wJo61Z-JfF3OS0ng6ViRC18s=XEgU8Fh1wGcYqmtsBazRiOZIu0gUp1SLFYlLskyZLZE=
>



-- 
Jasmin Alves
Predoctoral Student
Medical Biology Graduate Program
University of Southern California
jal...@usc.edu
___
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] comparing multiple runs on the same scan

[Krieger, Donald N.]

It looks like they do give the same results.
I have to write something to go through everything systematically which I may 
not get to till tomorrow.
Also I am checking to see whether there was some difference in how 001.mgz was 
created.
The source image file on which we are running freesurfer is a defaced.mgz . 
It's possible that it was sitting in a different directory for the different 
runs since the runs were executed by a work flow management system (Pegasus) on 
the Open Science Grid.

Don


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 10, 2016 6:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] comparing multiple runs on the same scan

That probably means that there is something in the header that is
different. It should print a report to the terminal. Do they not give
the same results?

On 02/10/2016 04:36 PM, Krieger, Donald N. wrote:
> mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are 
> different.
> In fact, their sizes are slightly different.
>
>
>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
>> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
>> Sent: Wednesday, February 10, 2016 3:45 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
>>
>> Hi Don
>>
>> are you saying the 001.mgz is different when created from the same dicom
>> data? Can you run mri_diff on it to see what the difference is?
>>
>> cheers
>> Bruce
>> On Wed, 10
>> Feb 2016, Krieger, Donald N. wrote:
>>
>>> We would like to confirm that we are getting identical results from
>>> multiple freesurfer runs on the same data set.
>>>
>>> To do so we are comparing identically named files using md5sum and
>>> would very much appreciate your thoughts on our results.  For multiple
>>> files, we concatenate them and pipe the output into md5sum.  Below is
>>> a table showing what we’ve found so far.  I take hope from the
>>> positive matches we get from all of the .annot files and from the fact
>>> that 001.mgz does not match.  This latter suggests that there is a
>>> date or something embedded in some of the files from separate runs which
>> defeats the match.
>>>
>>>
>>> Please let us know what you know about this and thanks.
>>>
>>>
>>>
>>> file(s)
>>>
>>> md5sum result
>>>
>>> label/*.annot
>>>
>>> match
>>>
>>> label/*.label
>>>
>>> match
>>>
>>> mri/wmparc.mgz
>>>
>>> mismatch
>>>
>>> surf/qsphere.nofix
>>>
>>> surf/rh.sphere
>>>
>>> mismatch
>>>
>>> mri/orig/001.mgz
>>>
>>> mismatch
>>>
>>> mri/transforms/talairach.m3z
>>>
>>> match
>>>
>>> mri/transforms/talairach.m3z.inv.x.mgz
>>>
>>> mri/transforms/talairach.m3z.inv.y.mgz
>>>
>>> mri/transforms/talairach.m3z.inv.z.mgz
>>>
>>> mismatch
>>>
>>> mismatch
>>>
>>> mismatch
>>>
>>>
>>>
>>> Best - Don
>>>
>>>
>>>
>>>
>>>
>>> Don Krieger, Ph.D.
>>>
>>> Department of Neurological Surgery
>>>
>>> University of Pittsburgh
>>>
>>>
>>>
> ___
> 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.

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

Re: [Freesurfer] comparing multiple runs on the same scan

[Douglas N Greve]

That probably means that there is something in the header that is 
different. It should print a report to the terminal. Do they not give 
the same results?

On 02/10/2016 04:36 PM, Krieger, Donald N. wrote:
> mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are 
> different.
> In fact, their sizes are slightly different.
>
>
>
>> -Original Message-
>> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
>> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
>> Sent: Wednesday, February 10, 2016 3:45 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
>>
>> Hi Don
>>
>> are you saying the 001.mgz is different when created from the same dicom
>> data? Can you run mri_diff on it to see what the difference is?
>>
>> cheers
>> Bruce
>> On Wed, 10
>> Feb 2016, Krieger, Donald N. wrote:
>>
>>> We would like to confirm that we are getting identical results from
>>> multiple freesurfer runs on the same data set.
>>>
>>> To do so we are comparing identically named files using md5sum and
>>> would very much appreciate your thoughts on our results.  For multiple
>>> files, we concatenate them and pipe the output into md5sum.  Below is
>>> a table showing what we’ve found so far.  I take hope from the
>>> positive matches we get from all of the .annot files and from the fact
>>> that 001.mgz does not match.  This latter suggests that there is a
>>> date or something embedded in some of the files from separate runs which
>> defeats the match.
>>>
>>>
>>> Please let us know what you know about this and thanks.
>>>
>>>
>>>
>>> file(s)
>>>
>>> md5sum result
>>>
>>> label/*.annot
>>>
>>> match
>>>
>>> label/*.label
>>>
>>> match
>>>
>>> mri/wmparc.mgz
>>>
>>> mismatch
>>>
>>> surf/qsphere.nofix
>>>
>>> surf/rh.sphere
>>>
>>> mismatch
>>>
>>> mri/orig/001.mgz
>>>
>>> mismatch
>>>
>>> mri/transforms/talairach.m3z
>>>
>>> match
>>>
>>> mri/transforms/talairach.m3z.inv.x.mgz
>>>
>>> mri/transforms/talairach.m3z.inv.y.mgz
>>>
>>> mri/transforms/talairach.m3z.inv.z.mgz
>>>
>>> mismatch
>>>
>>> mismatch
>>>
>>> mismatch
>>>
>>>
>>>
>>> Best - Don
>>>
>>>
>>>
>>>
>>>
>>> Don Krieger, Ph.D.
>>>
>>> Department of Neurological Surgery
>>>
>>> University of Pittsburgh
>>>
>>>
>>>
> ___
> 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] difference in 001.mgz found

[Bruce Fischl]

yes, we store the command lines used to generate a .mgz in the header, so 
that makes sense

Bruce
On Thu, 11 Feb 2016, Krieger, Donald N. wrote:


These runs were executed on the Open Science Grid.
So the data file, the scan, was uploaded to grid worker machine, placed in a 
transitory directory, and processed.
The full pathname of the file is included in 001.mgz.
I got it by: zcat mri/orig/001.mgz | strings
Here are the input and output file names for 2 of the runs:
/var/lib/condor/execute/dir_31034/MRN_1_defaced.mgz
/scratch/tmp.FFTGBhmgp8/MRN_1/mri/orig/001.mgz

/var/lib/condor/execute/dir_3734674/glide_HRFaAm/execute/dir_3741395/MRN_1_defaced.mgz
 /scratch/tmp.ghJfB4leGR/MRN_1/mri/orig/001.mgz

Best - Don



-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
boun...@nmr.mgh.harvard.edu] On Behalf Of Krieger, Donald N.
Sent: Wednesday, February 10, 2016 6:38 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] comparing multiple runs on the same scan

It looks like they do give the same results.
I have to write something to go through everything systematically which I may
not get to till tomorrow.
Also I am checking to see whether there was some difference in how 001.mgz
was created.
The source image file on which we are running freesurfer is a defaced.mgz .
It's possible that it was sitting in a different directory for the different 
runs
since the runs were executed by a work flow management system (Pegasus) on
the Open Science Grid.

Don


From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-
boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, February 10, 2016 6:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] comparing multiple runs on the same scan

That probably means that there is something in the header that is different. It
should print a report to the terminal. Do they not give the same results?

On 02/10/2016 04:36 PM, Krieger, Donald N. wrote:

mri_diff finds no differences in the mri/orig/001.mgz's but the checksums are

different.

In fact, their sizes are slightly different.




-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
Sent: Wednesday, February 10, 2016 3:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] comparing multiple runs on the same scan

Hi Don

are you saying the 001.mgz is different when created from the same
dicom data? Can you run mri_diff on it to see what the difference is?

cheers
Bruce
On Wed, 10
Feb 2016, Krieger, Donald N. wrote:


We would like to confirm that we are getting identical results from
multiple freesurfer runs on the same data set.

To do so we are comparing identically named files using md5sum and
would very much appreciate your thoughts on our results.  For
multiple files, we concatenate them and pipe the output into md5sum.
Below is a table showing what we’ve found so far.  I take hope from
the positive matches we get from all of the .annot files and from
the fact that 001.mgz does not match.  This latter suggests that
there is a date or something embedded in some of the files from
separate runs which

defeats the match.



Please let us know what you know about this and thanks.



file(s)

md5sum result

label/*.annot

match

label/*.label

match

mri/wmparc.mgz

mismatch

surf/qsphere.nofix

surf/rh.sphere

mismatch

mri/orig/001.mgz

mismatch

mri/transforms/talairach.m3z

match

mri/transforms/talairach.m3z.inv.x.mgz

mri/transforms/talairach.m3z.inv.y.mgz

mri/transforms/talairach.m3z.inv.z.mgz

mismatch

mismatch

mismatch



Best - Don





Don Krieger, Ph.D.

Department of Neurological Surgery

University of Pittsburgh




___
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.

___
Freesurfer mailing list

Re: [Freesurfer] difference in 001.mgz found

[Krieger, Donald N.]

Thanks for the confirmation, Bruce.
I've looked at  the other files I spot checked which failed to match.
A bunch of the files in directory surf contain a line at the top like "Created 
by nobody on Mon Feb 8 15:13:58 2016"
The mri/transforms/talairach.m3z.inv.?.mgz files contain the pathname of a  
.xfm file.
I'm pretty confident now that we are getting the same results from all the runs 
but I want write something to check systematically.

Best - Don

> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
> Sent: Wednesday, February 10, 2016 8:15 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] difference in 001.mgz found
> 
> yes, we store the command lines used to generate a .mgz in the header, so that
> makes sense Bruce On Thu, 11 Feb 2016, Krieger, Donald N. wrote:
> 
> > These runs were executed on the Open Science Grid.
> > So the data file, the scan, was uploaded to grid worker machine, placed in a
> transitory directory, and processed.
> > The full pathname of the file is included in 001.mgz.
> > I got it by: zcat mri/orig/001.mgz | strings Here are the input and
> > output file names for 2 of the runs:
> > /var/lib/condor/execute/dir_31034/MRN_1_defaced.mgz
> > /scratch/tmp.FFTGBhmgp8/MRN_1/mri/orig/001.mgz
> >
> > /var/lib/condor/execute/dir_3734674/glide_HRFaAm/execute/dir_3741395/M
> > RN_1_defaced.mgz /scratch/tmp.ghJfB4leGR/MRN_1/mri/orig/001.mgz
> >
> > Best - Don
> >
> >
> >> -Original Message-
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> >> boun...@nmr.mgh.harvard.edu] On Behalf Of Krieger, Donald N.
> >> Sent: Wednesday, February 10, 2016 6:38 PM
> >> To: Freesurfer support list
> >> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> >>
> >> It looks like they do give the same results.
> >> I have to write something to go through everything systematically
> >> which I may not get to till tomorrow.
> >> Also I am checking to see whether there was some difference in how
> >> 001.mgz was created.
> >> The source image file on which we are running freesurfer is a defaced.mgz .
> >> It's possible that it was sitting in a different directory for the
> >> different runs since the runs were executed by a work flow management
> >> system (Pegasus) on the Open Science Grid.
> >>
> >> Don
> >>
> >> 
> >> From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-
> >> boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve
> >> [gr...@nmr.mgh.harvard.edu]
> >> Sent: Wednesday, February 10, 2016 6:13 PM
> >> To: freesurfer@nmr.mgh.harvard.edu
> >> Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> >>
> >> That probably means that there is something in the header that is
> >> different. It should print a report to the terminal. Do they not give the 
> >> same
> results?
> >>
> >> On 02/10/2016 04:36 PM, Krieger, Donald N. wrote:
> >>> mri_diff finds no differences in the mri/orig/001.mgz's but the
> >>> checksums are
> >> different.
> >>> In fact, their sizes are slightly different.
> >>>
> >>>
> >>>
>  -Original Message-
>  From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
>  boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl
>  Sent: Wednesday, February 10, 2016 3:45 PM
>  To: Freesurfer support list
>  Subject: Re: [Freesurfer] comparing multiple runs on the same scan
> 
>  Hi Don
> 
>  are you saying the 001.mgz is different when created from the same
>  dicom data? Can you run mri_diff on it to see what the difference is?
> 
>  cheers
>  Bruce
>  On Wed, 10
>  Feb 2016, Krieger, Donald N. wrote:
> 
> > We would like to confirm that we are getting identical results
> > from multiple freesurfer runs on the same data set.
> >
> > To do so we are comparing identically named files using md5sum and
> > would very much appreciate your thoughts on our results.  For
> > multiple files, we concatenate them and pipe the output into md5sum.
> > Below is a table showing what we’ve found so far.  I take hope
> > from the positive matches we get from all of the .annot files and
> > from the fact that 001.mgz does not match.  This latter suggests
> > that there is a date or something embedded in some of the files
> > from separate runs which
>  defeats the match.
> >
> >
> > Please let us know what you know about this and thanks.
> >
> >
> >
> > file(s)
> >
> > md5sum result
> >
> > label/*.annot
> >
> > match
> >
> > label/*.label
> >
> > match
> >
> > mri/wmparc.mgz
> >
> > mismatch
> >
> > surf/qsphere.nofix
> >
> > surf/rh.sphere
> >
> > mismatch
> >
> > mri/orig/001.mgz
> >
> > mismatch
> >
> >