[Freesurfer] hippocampal subfields

[Ferdi van de Kamp]

Hi all,

I'm trying to perform the longitudinal hippocampal subfields processing on
a cluster.

When I simply access a core on the cluster directly and use it to run the
hippocampal subfields it will run, but if I try to submit the process to
the cluster, it will either throw errors as I have pasted below or stop
after some registration steps.

The recon-all steps have run on the cluster (submitted) without problems.

Some notes:
As I'm testing things, the data is not in the original folder, so the path
names in recon-all log are not correct, but if that is the problem I'd
imagine it would be a problem for both submitting and direct processing.

Matlab runtime is installed, though in a separate folder, linking it in the
way described on the Freesurfer website.

The problem persists no matter how much memory I allocate to the process
(20GB RAM was the highest I tried).


Kind regards,

Ferdi van de Kamp



#
#@# Longitudinal Hippocampal Subfields processing (T1) left Wed Jan  4
03:06:40 CET 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/runtime/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/bin/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/os/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/OpenGridScheduler/gridengine/lib/linux-x64/:/usr/local/jemalloc/current/lib/:/usr/local/lib/:/usr/local/ScaLAPACK/scalapack-2.0.2/lib/
Warning: Unable to open display 'localhost:10.0'.  You will not be able to
display graphics on the screen.
Registering imageDump.mgz to hippocampal mask from ASEG of Base Point
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop:
line 3: 65931 Segmentation fault  (core dumped) kvlAutoCrop.bin "$@"
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin//kvlAutoCrop
/exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_left//hippoAmygBinaryMask.mgz
6 >/dev/null: Segmentation fault
gzip:
/exports/fsw/MBos/DevTest/P0392Base/tmp/hippoSF_T1_long.v10_left//hippoAmygBinaryMask_autoCropped.mgz.gz:
No such file or directory
ERROR: problem reading fname
SWITCH expression must be a scalar or string constant.

Error in myMRIread>load_mgh (line 550)



Error in myMRIread>myMRIread_aux (line 92)



Error in myMRIread (line 63)



Error in SegmentSubfieldsT1Longitudinal (line 228)



MATLAB:badSwitchExpression
@#@FSTIME  2017:01:04:03:06:40
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh
N 8 e 12.17 S 0.80 U 3.63 P 36% M 680932 F 530 R 118193 W 0 c 10055 w 5994
I 439360 O 194448 L 4.58 4.59 4.59
@#@FSLOADPOST 2017:01:04:03:06:52
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//bin/segmentSF_T1_long.sh
N 8 4.72 4.62 4.60
#
#@# Longitudinal Hippocampal Subfields processing (T1) right Wed Jan  4
03:06:52 CET 2017
--
Setting up environment variables
---
LD_LIBRARY_PATH is
.:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/runtime/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/bin/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/os/glnxa64:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/local/OpenGridScheduler/gridengine/lib/linux-x64/:/usr/local/jemalloc/current/lib/:/usr/local/lib/:/usr/local/ScaLAPACK/scalapack-2.0.2/lib/
Warning: Unable to open display 'localhost:10.0'.  You will not be able to
display graphics on the screen.
Registering imageDump.mgz to hippocampal mask from ASEG of Base Point
/usr/local/Freesurfer/freesurfer-Linux-centos6_x86_64-stable-v6-beta/freesurfer//b

[Freesurfer] Editing annot files

[Martin Juneja]

Hi,

I was wondering if there is any way to edit annot file e.g. I would like to
edit *lh.Yeo2011_7Networks_N1000.annot* file in such a way when I overlay
this file in freeview, I just display limbic network from Yeo 7 network
atlas and hide other 6 networks.

I would prefer to use MATLAB for this but would really appreciate any other
simple way to do that.

Thanks.
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Re: [Freesurfer] reposition surface for pial surface

[Antonin Skoch]

Dear Paul,

I cannot see your attachment since I am only getting mail digest (without 
attachments) and the mail archive does not store attachments.

I do not know for which option of surface reposition your question refers to. 
But, I hope when you play with the tool, you will figure out, as I did.

Also, what do you mean, what step you should start?
In case of "volume based" reposition, when you click on "apply", you internally 
invoke customized mris_make_surfaces code on the surface you want to modify. 
The run takes several seconds and when it is finished, you will see the result 
of reposition. Then you inspect the surface and when you are satisfied, you 
save the modified surface (by the proper name, i.e. overwriting the original 
surface, you can save it by different name before using this tool to be able to 
get back). Then you should rerun remaining steps of recon-all, which for 
example in case of V6beta after repositioning pial surface means running

recon-all -s my_subject -cortribbon -parcstats -cortparc2 -parcstats2 
-cortparc3 -pctsurfcon -hyporelabel -aparc2aseg -apas2aseg -segstats -wmparc 
-balabels

Antonin

Thank you very much Antonin. I do appreciate it. Do I need to insert a
vertex number or just the coordinates? Because when i clicked on the
surface outside the pial (see screenshot) the vertex = N/A ( see
screenshot). ALso, what step of recon-all should i start? (autorecon-2 or
autorecon3)?
Best,
PaulOn Tue, Jan 10, 2017 at 3:52 PM, Antonin Skoch  wrote:

> Dear Paul,
>
> I could chime in with my current limited experiences with this tool (using
> V6beta version of freeview). Maybe they could be helpful for you.
>
> Most straigthforward is using "edit coordinate":
>
> Select the surface you want to edit.
> Select tools-reposition surface - edit coordinate.
> With shift + left mouse button click on the surface to pick particular
> vertex.
> Manually enter new coordinates of the vertex.
> Save surface to store edits.
> This is prohibitively time consuming in case of large error, so it is
> usable only in case of small errors.
>
> However, you can try to use combination of "edit coordinate" and "smooth".
> By smoothing you can nudge some area of adjacent vertices to desired
> position.
>
> I was partially successful  also with using
> reposition surface - volume based - coordinate:
> With shift + left mouse button select particular vertex
> In "volumes", load volume according to what you want to reposition the
> surface.
> With shift + ctrl + left mouse button click at the coordinate you want to
> reposition the surface to.
> Save surface to store edits.
>
> Regarding the parameters:
> The "size" textfield determine the extent of the vertex neighbourhood
> which would be repositioned. Do not use too large value since then the
> behaviour is unpredictable, in my case the maximal resonable value is
> around 5.
> I am not sure about "sigma" parameter, maybe it has to do something with
> the smoothing (of the underlying volume?),  however in my case altering
> this parameter did not change behaviour much.
> Also, the "gradient direction" in my case did not change much, in many
> cases it produced identical result regardless of the gradient direction
> selected.
>
> In most cases, I was not satisfied with the result of the reposition, the
> particular vertex moved to desired position, however position of adjacent
> vertices did not make sense, mostly the surface got very jagged and
> irregular, with worsening of the position in areas where the position was
> good previously, etc. However, subsequent using of "smooth" usually
> improved the shape and after many iterations I finally arrived to desired
> shape of surface.
>
> I also tried to study the relevant source code to learn the behavior of
> this tool and the significance of the parameters, but it is very
> complicated to me to comprehend (so far..).
>
> Note that after using this tool you should rerun remaining code of
> recon-all
>
> ReconAllDevTable
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
> (for development version) would tell you which particular steps should be
> rerun.
> Please note that in case of  rerun of recon-all from start you will lose
> all modifications of surfaces you achieved using this tool.
>
> And, particularly, many surface errors can be corrected by editing the
> volume (particularly wm.mgz, brainmask.mgz, aseg.mgz) or adding control
> points to the white matter.
> Large errors of ?h.white (and subsequently ?h.pial) can be caused of
> wrongly corrected topological defect (which you can diagnose by inspecting
> ?h.orig.nofix and ?h.orig). In that case editing of wm.mgz or aseg.mgz
> would help to correct the issue.
> I also came across the error when ?h.white was cut off the particular
> gyrus near midline, which was caused by erroneous labeling of cortex in
> aseg.mgz (gyrus was attributed to contralateral hemisphere). Editing of
> aseg.mgz by assignment of the gyrus to correct hemisphere corre

Re: [Freesurfer] Interaction effects in QDEC

[Douglas N Greve]

This is done automatically when you have two categorical variables and 
two continuous variables. This is equivalent to asking whether the two 
slopes differ across the two categorical variables.


On 01/07/2017 09:30 AM, Heidi Foo wrote:
> Hi all,
>
> I was wondering how I could test for interaction effects between a 
> categorical variable and a continuous variable using QDEC. Is there a 
> way to do so?
>
> Thank you.
>
> Best Regards,
> Heidi Foo
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
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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
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Re: [Freesurfer] Is the average surface in MNI space?

[Douglas N Greve]

On 01/07/2017 06:19 AM, Ling Zhao wrote:
>
> *Dear experts,*
>
> 1.From the FreeSufer wiki we all knows all of the processing and the 
> generated files are in the Talairach (MNI305) coordinate. The 
> FreeSurfer operates 
> in a conformed space, which is different from the original structural 
> image space that it has received as an input. If I want to use the 
> generated surfaces or labels as masks (which is inTalairach space) for 
> DTI probtrackx (which is need in diffusion space). How should I do?
>
Which wiki page says that? Actually all of the processing is done in 
native (albeit "conformed") native anatomical space. To use the labels 
in a DTI analysis, you'll need to register the DTI (low-b volume) to the 
freesurfer subject (bbregister), then use mri_label2vol to map a 
segmentation (eg, aparc+aseg.mgz) into the DTI space. See the multimodal 
tutorial.
>
> 2.In your wikiI see the information as following:
>
> “*Average Surface Construction*
>
> The average surface is constructed by computing the Talairach (MNI305) 
> coordinate at each vertex for each subject (based on the talairach.xfm 
> matrix for that subject). These coordinates are then mapped into the 
> common surface space and averaged together so that the coordinate of a 
> vertex in the common surface space is the average of the Talairach 
> coordinates from the corresponding surface locations of the 
> individuals. This results in the average surface overlaying nicely on 
> the average (MNI305) volume. ”
>
> Is the MNI305 in the MNI space? Can you tell me the meaning of the 
> MNI305 in “Talairach (MNI305) coordinate”?
>
> After the average surface overlaying nicely on the average (MNI305) 
> volume. Is the average surface in the MNI space or in the Talairach 
> space / common surface space?
>
It is in MNI305 space which is defined by the MNI305 average brain. This 
is similar to the MNI152 space (the "standard" MNI space) but not 
identical. We also report a "Talairach" space coordinate. This is 
computed by applying a formula to the MNI305 coordinates
>
> Best wishes
>
> Ling Zhao
>
>
> --
>
> Center for the Study of Applied Psychology, Key Laboratory of Mental Health 
> and Cognitive Science of Guangdong Province, School of Psychology, South 
> China Normal University, Guangzhou 510631, P. R. China
>
>
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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

Re: [Freesurfer] reposition surface for pial surface

[miracle ozzoude]

Thank you very much Antonin. I do appreciate it. Do I need to insert a
vertex number or just the coordinates? Because when i clicked on the
surface outside the pial (see screenshot) the vertex = N/A ( see
screenshot). ALso, what step of recon-all should i start? (autorecon-2 or
autorecon3)?
Best,
Paul

On Tue, Jan 10, 2017 at 3:52 PM, Antonin Skoch  wrote:

> Dear Paul,
>
> I could chime in with my current limited experiences with this tool (using
> V6beta version of freeview). Maybe they could be helpful for you.
>
> Most straigthforward is using "edit coordinate":
>
> Select the surface you want to edit.
> Select tools-reposition surface - edit coordinate.
> With shift + left mouse button click on the surface to pick particular
> vertex.
> Manually enter new coordinates of the vertex.
> Save surface to store edits.
> This is prohibitively time consuming in case of large error, so it is
> usable only in case of small errors.
>
> However, you can try to use combination of "edit coordinate" and "smooth".
> By smoothing you can nudge some area of adjacent vertices to desired
> position.
>
> I was partially successful  also with using
> reposition surface - volume based - coordinate:
> With shift + left mouse button select particular vertex
> In "volumes", load volume according to what you want to reposition the
> surface.
> With shift + ctrl + left mouse button click at the coordinate you want to
> reposition the surface to.
> Save surface to store edits.
>
> Regarding the parameters:
> The "size" textfield determine the extent of the vertex neighbourhood
> which would be repositioned. Do not use too large value since then the
> behaviour is unpredictable, in my case the maximal resonable value is
> around 5.
> I am not sure about "sigma" parameter, maybe it has to do something with
> the smoothing (of the underlying volume?),  however in my case altering
> this parameter did not change behaviour much.
> Also, the "gradient direction" in my case did not change much, in many
> cases it produced identical result regardless of the gradient direction
> selected.
>
> In most cases, I was not satisfied with the result of the reposition, the
> particular vertex moved to desired position, however position of adjacent
> vertices did not make sense, mostly the surface got very jagged and
> irregular, with worsening of the position in areas where the position was
> good previously, etc. However, subsequent using of "smooth" usually
> improved the shape and after many iterations I finally arrived to desired
> shape of surface.
>
> I also tried to study the relevant source code to learn the behavior of
> this tool and the significance of the parameters, but it is very
> complicated to me to comprehend (so far..).
>
> Note that after using this tool you should rerun remaining code of
> recon-all
>
> ReconAllDevTable
> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
> (for development version) would tell you which particular steps should be
> rerun.
> Please note that in case of  rerun of recon-all from start you will lose
> all modifications of surfaces you achieved using this tool.
>
> And, particularly, many surface errors can be corrected by editing the
> volume (particularly wm.mgz, brainmask.mgz, aseg.mgz) or adding control
> points to the white matter.
> Large errors of ?h.white (and subsequently ?h.pial) can be caused of
> wrongly corrected topological defect (which you can diagnose by inspecting
> ?h.orig.nofix and ?h.orig). In that case editing of wm.mgz or aseg.mgz
> would help to correct the issue.
> I also came across the error when ?h.white was cut off the particular
> gyrus near midline, which was caused by erroneous labeling of cortex in
> aseg.mgz (gyrus was attributed to contralateral hemisphere). Editing of
> aseg.mgz by assignment of the gyrus to correct hemisphere corrected the
> error.
>
> Also, altering several of global parameters of mris_make_surfaces, as
> listed for example here
>
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37990.html
>
> could help you to get satisfactory results (however, the altering of these
> parameters should be done in my opinion for all subjects in the study to
> avoid bias).
>
> Regards,
>
> Antonin
>
> Thanks bruce for your response. Since there is no documentation, how can i
> use it because I seen trends on the forum where it was suggested to use
> reposition surface ( 
> e.g.https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026117.html).
> Use = directions and parameters to input. Thanks
> Best,
> Paul
>
> On Tue, Jan 10, 2017 at 12:42 PM, Bruce Fischl 
> wrote:
>
> > Hi Paul
> >
> > sorry, this is something that Ruopeng put together for me to mess around
> > with - there isn't any documentation
> >
> > cheers
> > Bruce
> >
> > On Tue, 10 Jan 2017, miracle ozzoude wrote:
> >
> > Hello Freesurfer, I would like to learn how to use the reposition surface
> >> tool in freeview. Specifically, what parameters to enter in the 

Re: [Freesurfer] Help - Error: cannot unpack mosaics without ASCII header

[Douglas N Greve]

Not sure. Can you upload the set to

  https://gate.nmr.mgh.harvard.edu/filedrop2

and I'll take a look

On 01/10/2017 03:31 PM, Caleb Comoglio wrote:
> Hello,
>
> I am having trouble with the MRI_convert portion of recon-all. I get 
> the error below when I run recon-all and when I run MRI_convert 
> independently of recon-all.
>
> WARNING: file Desktop/3T_20161201_131733544/MR04 does not contain 
> a Siemens ASCII header
>
> has this file been anonymized?
>
> ERROR: cannot unpack mosiacs without ASCII header
>
>
> Prior to getting the error I get the following message:
> *
> *
>
> Scanning Directory
>
> INFO: Found 2316 files in Desktop/3T_20161201_131733544
>
> INFO: Scanning for Series Number 2
>
> INFO: found 192 files in series
>
> INFO: loading series header info.
>
>
> INFO: sorting.
>
> RunNo = 1
>
> WARNING: Run 1 appears to be truncated
>
>   Files Found: 192, Files Expected (lRep+1): 1
>
>
> Do you have any suggestions? Additional system info is below:
> 1) OS: MacOS Sierra (10.12.2)
> 2) FS software version: freesurfer-Darwin-lion-stable-pub-v5.3.0
> 3) Data is MPRAGE directly from a siemens machine
> *
> *
> *Caleb C. Comoglio, BSBME
> *
> Graduate Research Fellow
> Bioelectronics Laboratory, IUPUI
> ccomo...@iupui.edu 
> (574) 727-1620
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

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

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

Re: [Freesurfer] Multiple comparison correction on subcortical volume

[Douglas N Greve]

I would say yes, but I've seen plenty of pubs that do not correct. The 
bonferroni correction is fine. You could also try FDR (though on 4 
points it might not make much sense).


On 01/10/2017 01:47 PM, neuroimage analyst wrote:
> Hi,
>
> I extracted thalamic, caudate, and putamen volume (left hemisphere), 
> and cingulate thickness (right hemisphere) from 
> freesurfer's parcellation. Then I compare these volumes and thickness 
> across two groups using R and found significant differences in these 
> measurements. Do I have to correct for multiple comparisons?
>
> If yes, how do I do that? Does this make sense to divide the p-value/4 
> and if the p-value < p-value/4 then the test is Bonferroni corrected? 
> If no, what do I say in my results that the test statistic is not 
> inflated?
>
> Thanks
>
> Regards
>
> --VM
>
>
> ___
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] autorecon1 crash (with nu_correct).

[Douglas N Greve]

Is this happening on all your subjects or just this one? If just this 
one, have you looked at the image to see if it looks ok?


On 01/10/2017 01:09 PM, Jamie Hanson wrote:
> Hello Freesurfer List,
>
> I was running into issues processing subjects, with errors just 
> getting through the autorecon1 step of the pipeline. My terminal 
> outputs the following:
>
> 
>
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri
> /usr/local/pkg/freesurfer-dev//bin/mri_nu_correct.mni
> --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 
> --distance 50
> nIters 1
> $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
> Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 
> x86_64 x86_64 x86_64 GNU/Linux
> Tue Jan 10 12:53:44 EST 2017
> Program nu_correct, built from:
> Package MNI N3, version 1.10, compiled by nicks@minerva 
> (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
> /usr/bin/bc
> tmpdir is ./tmp.mri_nu_correct.mni.129237
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri
> mri_convert orig.mgz ./tmp.mri_nu_correct.mni.129237/nu0.mnc -odt float
> mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.129237/nu0.mnc -odt 
> float
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
> reading from orig.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, -1.32349e-23, -1.32349e-23)
> j_ras = (0, 1.49012e-08, -1)
> k_ras = (0, 1, 1.49012e-08)
> changing data type from uchar to float (noscale = 0)...
> writing to ./tmp.mri_nu_correct.mni.129237/nu0.mnc...
>
> 
> Iteration 1 Tue Jan 10 12:53:47 EST 2017
> nu_correct -clobber ./tmp.mri_nu_correct.mni.129237/nu0.mnc 
> ./tmp.mri_nu_correct.mni.129237/nu1.mnc -tmpdir 
> ./tmp.mri_nu_correct.mni.129237/0/ -iterations 1000 -distance 50
> Can't use 'defined(@array)' (Maybe you should just omit the 
> defined()?) at 
> /usr/local/pkg/freesurfer//mni/bin/nu_estimate_np_and_em line 165.
> nu_correct: crashed while running nu_estimate_np_and_em (termination 
> status=65280)
> ERROR: nu_correct
> Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 
> x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s 10007 exited with ERRORS at Tue Jan 10 12:53:47 EST 2017
>
> For more details, see the log file 
> /home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/scripts/recon-all.log
> To report a problem, see 
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
> 
>
> 
>
> Searching the FS list, I saw that I originally thought this was an 
> incompatibility with the current stable Freesurfer version and the 
> most recent MNI tools. To troubleshoot that issue, I installed the dev 
> version of Freesurfer (as noted by this thread: 
> https://mail.nmr.mgh.harvard.edu/pipermail///freesurfer/2016-September/047734.html
>  
> ).
>  
> The error however still persists (even using the dev version). Anyone 
> else run into this issue or have thoughts about troubleshooting it? 
> Thanks much!
>
> Best,
> Jamie.
>
> -- 
> Jamie Hanson
> Assistant Professor, Psychology
> Research Scientist, Learning Research and Development Center
> University of Pittsburgh
> Personal website: jamiehanson.org 
>
>
>
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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[Freesurfer] reposition surface for pial surface

[Antonin Skoch]

Dear Paul,

I could chime in with my current limited experiences with this tool (using 
V6beta version of freeview). Maybe they could be helpful for you.

Most straigthforward is using "edit coordinate":

Select the surface you want to edit.
Select tools-reposition surface - edit coordinate.
With shift + left mouse button click on the surface to pick particular vertex.
Manually enter new coordinates of the vertex.
Save surface to store edits.
This is prohibitively time consuming in case of large error, so it is usable 
only in case of small errors.

However, you can try to use combination of "edit coordinate" and "smooth". By 
smoothing you can nudge some area of adjacent vertices to desired position. 

I was partially successful  also with using 
reposition surface - volume based - coordinate:
With shift + left mouse button select particular vertex
In "volumes", load volume according to what you want to reposition the surface. 
With shift + ctrl + left mouse button click at the coordinate you want to 
reposition the surface to.
Save surface to store edits.

Regarding the parameters:
The "size" textfield determine the extent of the vertex neighbourhood which 
would be repositioned. Do not use too large value since then the behaviour is 
unpredictable, in my case the maximal resonable value is around 5.
I am not sure about "sigma" parameter, maybe it has to do something with the 
smoothing (of the underlying volume?),  however in my case altering this 
parameter did not change behaviour much.
Also, the "gradient direction" in my case did not change much, in many cases it 
produced identical result regardless of the gradient direction selected.

In most cases, I was not satisfied with the result of the reposition, the 
particular vertex moved to desired position, however position of adjacent 
vertices did not make sense, mostly the surface got very jagged and irregular, 
with worsening of the position in areas where the position was good previously, 
etc. However, subsequent using of "smooth" usually improved the shape and after 
many iterations I finally arrived to desired shape of surface.

I also tried to study the relevant source code to learn the behavior of this 
tool and the significance of the parameters, but it is very complicated to me 
to comprehend (so far..).

Note that after using this tool you should rerun remaining code of recon-all

ReconAllDevTable
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
(for development version) would tell you which particular steps should be rerun.
Please  note that in case of  rerun of recon-all from start you will lose all  
modifications of surfaces you achieved using this tool.

And, particularly, many surface errors can be corrected by editing the volume 
(particularly wm.mgz, brainmask.mgz, aseg.mgz) or adding control points to the 
white matter.
Large errors of ?h.white (and subsequently ?h.pial) can be caused of wrongly 
corrected topological defect (which you can diagnose by inspecting 
?h.orig.nofix and ?h.orig). In that case editing of wm.mgz or aseg.mgz would 
help to correct the issue.
I also came across the error when ?h.white was cut off the particular gyrus 
near midline, which was caused by erroneous labeling of cortex in aseg.mgz 
(gyrus was attributed to contralateral hemisphere). Editing of aseg.mgz by 
assignment of the gyrus to correct hemisphere corrected the error.

Also, altering several of global parameters of mris_make_surfaces, as listed 
for example here

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg37990.html

could help you to get satisfactory results (however, the altering of these 
parameters should be done in my opinion for all subjects in the study to avoid 
bias).

Regards,

Antonin
Thanks bruce for your response. Since there is no documentation, how can i
use it because I seen trends on the forum where it was suggested to use
reposition surface ( e.g.
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026117.html).
Use = directions and parameters to input. Thanks
Best,
PaulOn Tue, Jan 10, 2017 at 12:42 PM, Bruce Fischl 
wrote:

> Hi Paul
>
> sorry, this is something that Ruopeng put together for me to mess around
> with - there isn't any documentation
>
> cheers
> Bruce
>
> On Tue, 10 Jan 2017, miracle ozzoude wrote:
>
> Hello Freesurfer, I would like to learn how to use the reposition surface
>> tool in freeview. Specifically, what parameters to enter in the gui (see
>> screenshots). Is there any documentation on how to use it if not, can
>> someone with experience work me through it. Thank you.
>> best,
>> Paul

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[Freesurfer] Help - Error: cannot unpack mosaics without ASCII header

[Caleb Comoglio]

Hello,

I am having trouble with the MRI_convert portion of recon-all. I get the
error below when I run recon-all and when I run MRI_convert independently
of recon-all.

WARNING: file Desktop/3T_20161201_131733544/MR04 does not contain a
Siemens ASCII header

has this file been anonymized?

ERROR: cannot unpack mosiacs without ASCII header


Prior to getting the error I get the following message:

Scanning Directory

INFO: Found 2316 files in Desktop/3T_20161201_131733544

INFO: Scanning for Series Number 2

INFO: found 192 files in series

INFO: loading series header info.


INFO: sorting.

RunNo = 1

WARNING: Run 1 appears to be truncated

  Files Found: 192, Files Expected (lRep+1): 1

Do you have any suggestions? Additional system info is below:
1) OS: MacOS Sierra (10.12.2)
2) FS software version: freesurfer-Darwin-lion-stable-pub-v5.3.0
3) Data is MPRAGE directly from a siemens machine


*Caleb C. Comoglio, BSBME*
Graduate Research Fellow
Bioelectronics Laboratory, IUPUI
ccomo...@iupui.edu
(574) 727-1620


recon-all.log
Description: Binary data
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Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream

[Martin Reuter]

Hi Tamara,

mvoing in and popping out sounds like a scaling problem. We do only rigid 
transforms, so the scaling would already be in your original inputs. If that is 
the case, it could mean that there was a scanner calibration or something that 
caused scaled images and that would not be good. It should however appear in 
all images that have the calibration in between time points. 

You can try to use mri_robust_register with the affine flag to see if any 
scaling is present in the rawavg.mgz images between the two time points (it 
should report scaling separately on the screen output), else use lta_diff with 
the appropriate flags. You can also look at the affininely registered images 
and see if it looks better. 

Anyway if there is global scaling in the images, I would try to investigate a 
where this comes from and also drop that image from the study.

Best, Martin

> On 09 Jan 2017, at 17:24, Tamara Tavares  wrote:
> 
> Hi Dr. Reuter,
> 
> Thank you for the clarification. 
> 
> The differences I am seeing are also in the T1.mgz file in the longitudinal 
> run folder. I assume it is okay to use the T1.mgz from the longitudinal 
> outputs as the original image as I can easily compare the same slice across 
> different time points?
> 
> Also, on a related note, I have two scans (time 1 and time 2) that doesn't 
> seem to align perfectly with the template or with each other. When I use the 
> opacity slider to transition from the template to time 1 it looks like the 
> brain is 'moving in'. When I transition from template to time 2 the brain 
> seems to 'pop out'. Similarly, when I transition from time 1 to time 2, it 
> looks like the brain is popping out. With my other images, there is a smooth 
> transition from time 1 to time 2 and a relatively smooth transition from the 
> template to the time points. Do you think this is problematic? 
> 
> Thank you again for your help.
> 
> Best,
> Tamara
> 
> 
> 
> Message: 4
> Date: Wed, 28 Dec 2016 11:20:36 +0100
> From: Martin Reuter  >
> Subject: Re: [Freesurfer] Brighter image at baseline vs. follow up
> using   longitudinal processing stream
> To: Freesurfer support list  >
> Message-ID:  >
> Content-Type: text/plain; charset=us-ascii
> 
> Hi Tamara,
> 
> three out of how many? I would probably remove those three as whatever you 
> measure in them could be driven by the acquisition differences, but it 
> depends on what acquisition differences you have. If it is only small 
> differences, like tiny deviations in the voxel size etc, it should be OK.
> 
> I have no idea where the other intensity differences could come from. If you 
> see them in the original inputs, maybe an MR physicist could take a look and 
> advise. If you have a concrete case where the inputs are OK, but you think 
> that in FS processed images show different contrast or intensities, I would 
> need to have those images to see if I can replicate that.
> 
> Best, Martin
> ___
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[Freesurfer] Multiple comparison correction on subcortical volume

[neuroimage analyst]

Hi,

I extracted thalamic, caudate, and putamen volume (left hemisphere), and
cingulate thickness (right hemisphere) from freesurfer's parcellation. Then
I compare these volumes and thickness across two groups using R and found
significant differences in these measurements. Do I have to correct for
multiple comparisons?

If yes, how do I do that? Does this make sense to divide the p-value/4 and
if the p-value < p-value/4 then the test is Bonferroni corrected? If no,
what do I say in my results that the test statistic is not inflated?

Thanks

Regards

--VM
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[Freesurfer] autorecon1 crash (with nu_correct).

[Jamie Hanson]

Hello Freesurfer List,

I was running into issues processing subjects, with errors just getting
through the autorecon1 step of the pipeline. My terminal outputs the
following:



/home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri
/usr/local/pkg/freesurfer-dev//bin/mri_nu_correct.mni
--no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000
--distance 50
nIters 1
$Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $
Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux
Tue Jan 10 12:53:44 EST 2017
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva
(x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
/usr/bin/bc
tmpdir is ./tmp.mri_nu_correct.mni.129237
/home/jamielh/Volumes/Hanson/Pardini_Projects/K_award/10007/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.129237/nu0.mnc -odt float
mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.129237/nu0.mnc -odt float
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, -1.32349e-23, -1.32349e-23)
j_ras = (0, 1.49012e-08, -1)
k_ras = (0, 1, 1.49012e-08)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.129237/nu0.mnc...


Iteration 1 Tue Jan 10 12:53:47 EST 2017
nu_correct -clobber ./tmp.mri_nu_correct.mni.129237/nu0.mnc
./tmp.mri_nu_correct.mni.129237/nu1.mnc -tmpdir
./tmp.mri_nu_correct.mni.129237/0/
-iterations 1000 -distance 50
Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at
/usr/local/pkg/freesurfer//mni/bin/nu_estimate_np_and_em line 165.
nu_correct: crashed while running nu_estimate_np_and_em (termination
status=65280)
ERROR: nu_correct
Linux pfc 4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016
x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 10007 exited with ERRORS at Tue Jan 10 12:53:47 EST 2017

For more details, see the log file /home/jamielh/Volumes/Hanson/
Pardini_Projects/K_award/10007/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.
edu/fswiki/BugReporting



Searching the FS list, I saw that I originally thought this was an
incompatibility with the current stable Freesurfer version and the most
recent MNI tools. To troubleshoot that issue, I installed the dev version
of Freesurfer (as noted by this thread: https://mail.nmr.mgh.
harvard.edu/pipermail///freesurfer/2016-September/047734.html). The error
however still persists (even using the dev version). Anyone else run into
this issue or have thoughts about troubleshooting it? Thanks much!

Best,
Jamie.

-- 
Jamie Hanson
Assistant Professor, Psychology
Research Scientist, Learning Research and Development Center
University of Pittsburgh
Personal website: jamiehanson.org
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Re: [Freesurfer] reposition surface for pial surface

[miracle ozzoude]

Thanks bruce for your response. Since there is no documentation, how can i
use it because I seen trends on the forum where it was suggested to use
reposition surface ( e.g.
https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026117.html).
Use = directions and parameters to input. Thanks
Best,
Paul

On Tue, Jan 10, 2017 at 12:42 PM, Bruce Fischl 
wrote:

> Hi Paul
>
> sorry, this is something that Ruopeng put together for me to mess around
> with - there isn't any documentation
>
> cheers
> Bruce
>
> On Tue, 10 Jan 2017, miracle ozzoude wrote:
>
> Hello Freesurfer, I would like to learn how to use the reposition surface
>> tool in freeview. Specifically, what parameters to enter in the gui (see
>> screenshots). Is there any documentation on how to use it if not, can
>> someone with experience work me through it. Thank you.
>> best,
>> Paul
>>
>>
>>
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>
>
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> 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.
>
>
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Re: [Freesurfer] reposition surface for pial surface

[Bruce Fischl]

Hi Paul

sorry, this is something that Ruopeng put together for me to mess around 
with - there isn't any documentation


cheers
Bruce
On Tue, 10 Jan 2017, miracle ozzoude 
wrote:



Hello Freesurfer, I would like to learn how to use the reposition surface
tool in freeview. Specifically, what parameters to enter in the gui (see
screenshots). Is there any documentation on how to use it if not, can
someone with experience work me through it. Thank you. 
best, 
Paul


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[Freesurfer] reposition surface for pial surface

[miracle ozzoude]

Hello Freesurfer,
I would like to learn how to use the reposition surface tool in freeview.
Specifically, what parameters to enter in the gui (see screenshots). Is
there any documentation on how to use it if not, can someone with
experience work me through it. Thank you.
best,
Paul
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Re: [Freesurfer] ERROR: fast_selxavg3() failed\n

[Douglas Greve]

It looks like your FS_OCTAVE_BIN env variable is set to that bin folder. 
This variable should be set to the octave executable


On 1/10/17 7:34 AM, Michael Schirner wrote:
> Dear experts,
>
> I'm attempting to perform step 6 in the FsFastTutorialV5.1
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel;
> "First-level Analysis using selxavg3-sess"), but get the following error
> when I run the selxavg3-sess command:
>
> --- octave output 
> LD_LIBRARY_PATH
> /homec/hbu23/hbu231/Software/Octave/3.8.2/lib:/homec/hbu23/hbu231/Software/Libraries/octave
> /homec/hbu23/hbu231/Software/Octave/3.8.2/bin: Permission denied.
> --
> ERROR: fast_selxavg3() failed\n
>
>
> I've searched the list and a similar error has been reported but the
> proposed solution did not work.
> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-April/044814.html)
>
> Specifically, it does not work despite the named directory and several
> enclosing directories received full read, execute and for tests even write
> permissions (also, as a test, the freesurfer folders received full
> permissions):
>
> drwxrwxrwx 2 hbu231 hbu23 512 Jan  9 16:52 bin
>
> As I’m attempting to run it on a supercomputer I cannot execute it as a
> superuser.
>
> Does anyone have any thoughts on how to solve this?
>
> Thanks!
>
> Michael
>
> ---
> 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
> 2) Platform:  CentOS Linux release 7.2.1511 3) uname -a: Linux jrl11
> 3.10.0-327.36.3.el7.x86_64 #1 SMP Mon Oct 24 16:09:20 UTC 2016 x86_64
> x86_64 x86_64 GNU/Linux
>
>
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>

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Re: [Freesurfer] surface based analysis (projfrac)

[Douglas Greve]

When you say in the corpus callosum, do you mean in WM? The 
surface-based analysis is only for cortical GM. If you mean in GM near 
the CC, then the analysis is appropriate. The projfrac parameter sets 
the sampling location between the white and pial surfaces where 0.5 
means half way.



On 1/10/17 8:07 AM, John Anderson wrote:

Dear FS experts,
I am working on surface based analysis using freesurfer. I want to 
inquire about the flag "projfrac" in the command "mris_preproc"
I ran voxel wise analysis including the same subjects. I found 
differnce between the groups in areas close to the corpus callosum. I 
want to get the same results using surface based analysis. If I use 
the projfrac=0.5 is this able to show the same results that I got in 
voxel wise analysis at the level of the corpus callosum. Do I need to 
use differnt number for projfrac ?

Thank you for any advice.

Best,
John


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[Freesurfer] surface based analysis (projfrac)

[John Anderson]

Dear FS experts,

I am working on surface based analysis using freesurfer. I want to inquire about the flag "projfrac" in the command "mris_preproc"

 

I ran voxel wise analysis including the same subjects. I found differnce between the groups in areas close to the corpus callosum. I want to get the same results using surface based analysis. If I use the projfrac=0.5 is this able to show the same results that I got in voxel wise analysis at the level of the corpus callosum. Do I need to use differnt number for projfrac ?

 

Thank you for any advice.


 

Best,
John
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[Freesurfer] ERROR: fast_selxavg3() failed\n

[Michael Schirner]

Dear experts,

I'm attempting to perform step 6 in the FsFastTutorialV5.1
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastFirstLevel;
"First-level Analysis using selxavg3-sess"), but get the following error
when I run the selxavg3-sess command:

--- octave output 
LD_LIBRARY_PATH
/homec/hbu23/hbu231/Software/Octave/3.8.2/lib:/homec/hbu23/hbu231/Software/Libraries/octave
/homec/hbu23/hbu231/Software/Octave/3.8.2/bin: Permission denied.
--
ERROR: fast_selxavg3() failed\n


I've searched the list and a similar error has been reported but the
proposed solution did not work.
(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-April/044814.html)

Specifically, it does not work despite the named directory and several
enclosing directories received full read, execute and for tests even write
permissions (also, as a test, the freesurfer folders received full
permissions):

drwxrwxrwx 2 hbu231 hbu23 512 Jan  9 16:52 bin

As I’m attempting to run it on a supercomputer I cannot execute it as a
superuser.

Does anyone have any thoughts on how to solve this?

Thanks!

Michael

---
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Platform:  CentOS Linux release 7.2.1511 3) uname -a: Linux jrl11
3.10.0-327.36.3.el7.x86_64 #1 SMP Mon Oct 24 16:09:20 UTC 2016 x86_64
x86_64 x86_64 GNU/Linux


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Re: [Freesurfer] automatic segmentation of hippocampal subregions in young children

[Iglesias Gonzalez, Eugenio]

Dear Tracy,

It is true that we haven’t validated our software on such a young population, 
but I believe that, at age four, the appearance of the brain is close enough to 
that of adults for automated techniques do a good job (e.g., FreeSurfer has 
been used on children scans in many studies). Having said that, QCing a bunch 
of cases would be appropriate. Tracing the subfields in vivo with our ex vivo 
protocol to enable direct comparison (e.g., Dice scores) is nearly impossible, 
but a visual assessment of whether the segmentation follows the anatomy should 
be sufficient.

Kind regards,

/Eugenio


Juan Eugenio Iglesias
ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 9 Jan 2017, at 20:03, Tracy Riggins 
mailto:rigg...@umd.edu>> wrote:

Dr. Inglesias

I am a developmental psychologist studying memory and brain development in 
early childhood at the University of Maryland. My lab has acquired whole-brain 
standard resolution T1-weighted scans and ultra-high resolution T2-weighted 
scans from 125 child participants aged 4-8 years.  We are using your automatic 
segmentation for hippocampal subregions to obtain volumes for assessment in our 
study.

As we write up the results for publication, I began to wonder if reviewers will 
ask for verification that the automatic segmentation is valid for our young age 
group. I know you tested Alzheimer's and an elderly sample in your paper, so I 
suspect it is valid for a variety of populations. But I am writing to inquire 
your thoughts on this issue.  Do you think verification is needed?  If so, 
would you suggest we hand trace a subset of our data to verify the automatic 
methods?  I would appreciate any advise as to how to best approach this.

Thank you, in advance, for your consideration of my inquiry.

Sincerely,
Tracy


Tracy Riggins, Ph.D.
Associate Professor
University of Maryland

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Re: [Freesurfer] dice coefficient computing

[N Saf]

Dear Bruce,

Thank you very much,you are a life saver..

Best,
Nazanin

On Mon, Jan 9, 2017 at 11:05 PM, Bruce Fischl 
wrote:

> yes, you can use mri_convert as follows:
>
> mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.resliced.mgz
>
> assuming the rawavg.mgz has the 208x176x176 dimensions (which it should)
>
> cheers
> Bruce
> On Mon, 9 Jan 2017, N Saf wrote:
>
> Dear Bruce,
>>
>> thank you for your fast reply ,I think I could not explain the problem
>> correctly . I want the number of slices in aseg file convert from
>> 256x256x256 to 208x176x176(the
>> subject size) so I can enable to compute the dice coefficient with my
>> Matlab code ? any suggestions how can I make it possible?
>>
>>
>> Best Regards,
>> Nazanin
>>
>> On Mon, Jan 9, 2017 at 5:51 PM, Bruce Fischl 
>> wrote:
>>   Hi Nazanin
>>
>>   all our segmentations are in subject space, so it should be pretty
>> straightforward
>>
>>   cheers
>>   Bruce
>>   On Mon, 9 Jan 2017, N Saf wrote:
>>
>> Dear freesurfers,
>>
>> I analysis my T1 MRI with FreeSurfer (aseg.mgz 256x256x256)
>> and I have
>> manual segmentation for hippocampus in my subject
>> space(208x176x176)as well.
>> I want to compute the dice coefficient with one simple Matlab
>> code. how can
>> I do it correctly ?if I want to  bring the aseg to subject
>> space , which
>> command with which options is the best way to do it correctly
>> ?any help can
>> be appreciated.(I did it for the FSL segmentation result but
>> it was simple
>> because the result is in my subject space).
>>
>> Best Regards,
>> Nazanin
>>
>>
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>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
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