Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label

2019-02-21 Thread Yi Leng Fung 
External Email - Use Caution

Hello Bruce,

I am just checking in as I am curious if there has been any update
available regarding the entorhinal and perirhinal annot/labelling? I hope I
haven't missed anything.

Thank you!

Yi Leng

On Sun, Feb 10, 2019, 16:32 Yi Leng Fung 
wrote:

>
> Hello Bruce,
>
> I have uploaded a tarred and gzipped subject onto the ftp site. Do let me
> know if there is anything else I could help with.
>
> Cheers,
> Yi Leng
>
>
> On Sat, Feb 9, 2019 at 2:25 AM Bruce Fischl 
> wrote:
>
>> Hi Yi-Leng
>>
>> can you upload the worst subject to our ftp site (the entire gzipped and
>> tarred subject dir please).
>>
>> cheers
>> Bruce
>> On Fri, 8 Feb 2019, Yi Leng Fung wrote:
>>
>> >
>> > External Email - Use Caution
>> >
>> > [64b4f0f085b91c1f8130601d2cf65e8861fc5b7f.png?u=328927]
>> > Hello Bruce,
>> >
>> > On all four of our studies, the labels and the annot look similar in
>> the sense that almost the entire
>> > rh.perirhinal_exvivo.thresh.label was contained within the
>> rh.entorhinal_exvivo.thresh.label (screenshot of the
>> > right hemisphere with labels and annot attached for your reference).
>> The resulting annot label shows an extremely
>> > under-represented perirhinal on the right hemispheres. The left
>> hemispheres did not show such a dramatic overlap.
>> >
>> > Cheers,
>> > Yi-Leng
>> >
>> >
>> > On Fri, Feb 8, 2019 at 3:44 PM Bruce Fischl 
>> wrote:
>> > Do the labels look better than the annot?
>> >
>> > On Feb 6, 2019, at 10:15 PM, Yi Leng Fung 
>> wrote:
>> >
>> >   External Email - Use Caution
>> >
>> >   Hello FreeSurfer team,
>> >
>> > Thank you for providing the recon-all patch. We have applied this to
>> four studies and have seen a
>> > notable difference between in the representation of entorhinal over
>> perirhinal on the right hemisphere
>> > labelling on each analysis ran. The left hemisphere appears to have
>> less overlap.
>> >
>> > I have attached a screenshot of both hemispheres to demonstrate. Would
>> really appreciate any feedback.
>> > Thanks!
>> >
>> > Cheers,
>> > Yi-Leng
>> >
>> >
>> > On Wed, Feb 6, 2019 at 3:11 AM Hoopes, Andrew 
>> wrote:
>> >
>> >   Hi Yi Leng, there’s a recon-all patch for 6.0 at
>> >
>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/recon-all.
>> You can
>> >   update it with:
>> >
>> >
>> >
>> >   cd ${FREESURFER_HOME}/bin
>> >
>> >   mv recon-all recon-all.backup
>> >
>> >   curl
>> https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/recon-all
>> -o
>> >   recon-all
>> >
>> >   chmod +x recon-all
>> >
>> >
>> >
>> >   Let us know if that works!
>> >
>> >
>> >
>> >   thanks
>> >
>> >   Andrew
>> >
>> >
>> >
>> >   From:  on behalf of Yi
>> Leng Fung
>> >   
>> >   Reply-To: FS Help 
>> >   Date: Monday, February 4, 2019 at 9:17 PM
>> >   To: FS Help 
>> >   Cc: Jean Augustinack 
>> >   Subject: Re: [Freesurfer] Mismatch between ?h.BA.thresh.annot and
>> >   ?h.entorhinal.thresh.label/?h.perirhinal.thresh.label
>> >
>> >
>> >
>> > External Email - Use Caution
>> >
>> > Image removed by sender.
>> >
>> > Thank you!
>> >
>> >
>> >
>> > Cheers,
>> >
>> > Yi Leng
>> >
>> >
>> >
>> >
>> >
>> > On Tue, Feb 5, 2019 at 1:05 PM Bruce Fischl 
>> wrote:
>> >
>> >   thanks. It is almost certainly a bug in recon-all. I'm testing a
>> fix
>> >   tomorrow and hopefully we can have one out to you (and the rest
>> of the
>> >   list) by tomorrow.
>> >
>> >   Sorry!
>> >   Bruce
>> >   On Tue, 5 Feb 2019, Yi Leng Fung wrote:
>> >
>> >   >
>> >   > External Email - Use Caution
>> >   >
>> >   > [3a1715320c6fbab489126e656ad6e765d6e0a6ee.png?u=328927]
>> >   > Hello Bruce,
>> >   >
>> >   > Yep, the exvivo entorhinal thresh label overlay on the
>> perirhinal annotation. I
>> >   have attached a screenshot of it
>> >   > for your reference.
>> >   >
>> >   > Cheers,
>> >   > Yi-Leng
>> >   >
>> >   >
>> >   > On Tue, Feb 5, 2019 at 12:31 PM Bruce Fischl <
>> fis...@nmr.mgh.harvard.edu> wrote:
>> >   >   Hi Yi-Leng
>> >   >
>> >   >   eek! Can you verify that the
>> lh.entorhinal_exvivo.thresh.label is
>> >   >   correct? Does it overlay on the perirhinal annotation?
>> >   >
>> >   >   thanks
>> >   >   Bruce
>> >   >
>> >   >   On Tue, 5 Feb 2019,
>> >   >   Yi Leng Fung wrote:
>> >   >
>> >   >   >
>> >   >   > External Email - Use Caution
>> >   >   >
>> >   >   > [3f1a37b0d4514e4a90a5d3340afcefe6c789830e.png?u=328927]
>> >   >   > Hello All,
>> >   >   >
>> >   >   > Here it is, both are from bert.
>> >   >   >
>> >   >   > Thank you for looking into this.
>> >   >   >
>> >   >   > Cheers,
>> >   >   > Yi-Leng
>> >   >

[Freesurfer] Alignment to ACPC

2019-02-21 Thread Sadia Sheikh 
External Email - Use Caution

Hello Freesurfer experts

Freesurfer preprocessed data by(recon-all) are ACPC aligned?
If not how can I align my files to ACPC? I read the documents but I am
still very confused about the alignment and coordinate system in freesurfer.

Thanks in advance

Regards
Sadia
Research Student
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[Freesurfer] QDEC Longitudinal Analysis: Missing spc option from dropdown menu

2019-02-21 Thread Arsenije Subotic 
External Email - Use Caution

Dear Freesurfer experts,


I am having issues choosing the spc option for my QDEC two stage longitudinal 
analysis as it is not there. The spc files are all present in my participants 
files and the Qdecrc file is in the qdec subdirectory containing the line 
long.thickness-spc. Is there a way to bypass this problem somehow?


Thank you,

Arsenije


---

Arsenije Subotic | MSc Student

Department of Clinical Neurosciences

Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada

Tel: (403) 918-6970

arsenije.subot...@ucalgary.ca

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[Freesurfer] Issue posting to Freesurfer support

2019-02-21 Thread Daniel Callow 
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Hello,

I am signed up to post emails to Freesurfer support list <
freesurfer@nmr.mgh.harvard.edu> which I have cced in this email. However,
when I submit my questions they do not seem to show up or go to the
listserv. Is there someone I could contact to help with this?

Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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[Freesurfer] Data Analyst / Research Assistant Position at Child Mind Institute, New York {Disarmed}

2019-02-21 Thread Ting Xu 
External Email - Use Caution

*The Autism Center of the Child Mind Institute **is inviting applications **for
a Data Analyst position. The Data Analyst’s role is to assist and support
the acquisition, manipulation, and analysis of data, as well as the
reporting of brain imaging results. For more information click below.*


The Child Mind Institute makes use of innovative MRI-imaging approaches to
characterize brain maturation in typical and atypical development in
childhood with an explicit focus on understanding the impact of psychiatric
illnesses on maturational processes. Additionally, the Child Mind Institute
is dedicated to the support of open science projects such as the
International Neuroimaging Datasharing Initiative (
http://fcon_1000.projects.nitrc.org/

)
and the Configurable Pipeline for the Analysis of Connectomes (
http://fcp-indi.github.com). With this background a pplications are
currently being invited for Data Analyst position in the Autism Center. The
Data Analyst’s role is to assist and support the acquisition, manipulation,
and analysis of data, as well as the reporting results. In particular, our
work includes: 1) support the preprocessing of large fMRI dataset in
developing population, 2) maintain databases and imaging processing
pipeline 3) test and develop new features (e.g., denoising, segmentation,
etc.). 4) implement quality assurance protocols for imaging datasets.

Reporting to the Director of the Autism Center (*Director: Adriana Di
Martino*), this is an exempt, full-time positions located in our NYC
headquarters.

Responsibilities:

   - Implementation, execution and maintenance of fMRI imaging analysis
   pipelines
   - Exploration of novel software packages and problem-solving for issues
   with current and planned software packages
   - Develop graphs, reports, and presentations of project results
   - Mentoring of junior research staff in data analysis theory and
   implementation
   - Perform basic statistical analyses for projects and reports

Qualifications:

   - Master’s degree in neuroscience, computer science, mathematics,
   statistics or related areas.
   - Extensive neuroimaging experience in fMRI analysis and proficiency
   with one or more packages (e.g. FreeSurfer, AFNI, FSL, Workbench or SPM)
   - Programming experience in one or more languages (e.g., Python, Matlab,
   R or similar platforms is required).
   - Significant prior neuroimaging experience with more imaging and/or
   simulation modalities (e.g., DTI, EEG, MEG, TMS etc.) is a plus, but not
   required.
   - A passion for the Child Mind Institute mission

To apply: * 
https://workforcenow.adp.com/mascsr/default/mdf/recruitment/recruitment.html?cid=1b50a554-ed4a-4219-a358-aa3cbeea1e70=284229=en_US=CC3=19000101_01
*
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[Freesurfer] dt_recon registration check

2019-02-21 Thread Daniel Davidson Callow 
External Email - Use Caution

Hello,

I have run through dt_recon and want to use anatomically based
segmentations (aseg) to create ROIs for the diffusion-weighted data using
mri_vol2vol.

I ran

mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
$subj_dir/diffusion_recons/${subj}.${cond}/mri/aparc+aseg.mgz --inv
--interp nearest --o
$subj_dir/dtrecon/${subj}.${cond}./aparc+aseg2diff.nii.gz --reg
$subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg

Which worked.

I now want to quality check and make sure the ROIs I make from the
aseg2diff segmentation is accurately aligned in diffusion space (such as
making sure the hippocampal ROIs for aseg are actually going to overlay the
hippocampal region of the diffusion data). My question is what is the best
way to quality check for quality registration between the diffusion and
anatomical data?

Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
dcal...@umd.edu 
443-254-6298
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Re: [Freesurfer] recon-all -hires

2019-02-21 Thread Bruce Fischl 

Hi MOna


what was your full command line? And can you send us the recon-all.log 
file?


cheers
Bruce
On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote:



Dear Freesurfer experts


I was running recon-all command with hires flag for our high resolution fMRI 
data, but it has been in a
constant status since yesterday.

I copied the last few lines that are currently in my terminal. I had the same 
issue with another
subject before, and I had to terminate the recon-all and run it without -hires.

Could you please let me know how I can solve this issue?


Thanks

Mona



#@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019
/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts

 cp ../surf/rh.orig.nofix ../surf/rh.orig 


 cp ../surf/rh.inflated.nofix ../surf/rh.inflated 

#@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019

 mris_fix_topology 
-rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh 

#@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019

 mris_fix_topology 
-rusage/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.
rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh 

Waiting for PID 8994 of (8994 8997) to complete...




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Re: [Freesurfer] registration and resampling in native space

2019-02-21 Thread Francesca Strappini 
External Email - Use Caution

Thanks a lot!
Running preproc-sess with the --per-session flag is exactly was I was
looking for!
Now that my functional runs are correctly registered to a reference image
(so, to each other) I need to register them to a dataset of ROIs that were
created outside freesurfer. These regions are in volume space and have the
same resolution and box size of the functional runs. They are registered to
the T1 that was used for the reconstruction of the surface. I've tried
different functions for the registration but nothing really worked. I
suppose I need a registration matrix that relates these regions to the
reference image I used during the preprocessing and to apply this to each
region. What's the best procedure?

Best
Francesca


Il giorno gio 21 feb 2019 alle ore 19:39 Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> ha scritto:

> Yes,  if you run it with the --targ as orig.mgz for the given subject,
> then it will sample each run into the anatomical space (this can create
> enourmous data data files!). Alternatively, you can run preproc-sess
> with the --per-session flag and it will align all the runs to a single
> template but otherwise keep everything in the functional space
>
> On 2/20/19 11:53 AM, Francesca Strappini wrote:
> >
> > External Email - Use Caution
> >
> > I'll try to find some visual way to show what I mean, but it's really
> > something mild and probably negligible.
> > Do you know if is it possible with mri_vol2vol to give to all the runs
> > that belong to the same subject the same system coordinates? So that
> > each voxel across runs will have the same coordinates. I noticed that
> > the transformation matrix is written in the header but it's not really
> > applied to the data. Thank you!
> >
> >
> > Best
> > Francesca
> >
> >
> > On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl
> > mailto:fis...@nmr.mgh.harvard.edu>> wrote:
> >
> > Hi Francesca
> >
> > can you send us an image that shows why you think it can be improved?
> >
> > cheers
> > Bruce
> > On
> > Mon, 18 Feb 2019, Francesca Strappini wrote:
> >
> > >
> > > External Email - Use Caution
> > >
> > > Thank you!Now the registration is better but still not perfect.
> > Is there a way to improve it?
> > >
> > > Best
> > >
> > > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> ha
> > > scritto:
> > >   Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2
> > weighted? If so,
> > >   you should use --t2 instead of --t1 in bbregister
> > >
> > >   On 2/14/19 2:18 PM, Francesca Strappini wrote:
> > >   >
> > >   > External Email - Use Caution
> > >   >
> > >   > Hi Doug,
> > >   >
> > >   > Could you advise me about how to correctly run mri_vol2vol?
> > >   > The functional data did not get perfectly registered to
> > the anatomy so
> > >   > I'm afraid I'm not running it correctly.
> > >   >
> > >   > Thanks!
> > >   >
> > >   >
> > >   > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl
> > >   >  > 
> >  > >> ha
> > >   > scritto:
> > >   >
> > >   > Hi Francesca
> > >   >
> > >   > sorry, I defer to Doug on the details of mri_vol2vol.
> > >   >
> > >   > cheers
> > >   > Bruce
> > >   >
> > >   > On Tue, 12 Feb 2019,
> > >   > Francesca Strappini wrote:
> > >   >
> > >   > >
> > >   > > External Email - Use Caution
> > >   > >
> > >   > > Thank you for the reply!
> > >   > > I run:
> > >   > > mri_vol2vol --reg register.dat --mov
> > func_data.nii.gz --targ
> > >   > > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o
> > >   > func_data_registered2T1.nii.gz --no-resample
> > >   > >
> > >   > > Then I checked the registration and it seems that
> > the original
> > >   > run is better aligned to the T1 than
> > >   > > the registered one. Maybe am I not running
> > mri_vol2vol correctly?
> > >   > >
> > >   > > Thanks!
> > >   > > Best
> > >   > >
> > >   > >
> > >   > > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl
> > >   >  > 
> >  > >>
> > >   > ha scritto:
> > >   > >   Hi Francesca
> > >   > >
> > >   > >   check out the --no-resample

Re: [Freesurfer] mris_preproc error: dimension mismatch

2019-02-21 Thread Peters, Douglas G 
External Email - Use Caution

It turns out I could run qcache on a unique surface file in the subject's 
 folder. After a few tries with the surface file name it worked.

Using tcsh command line I ran qcache on all of my subjects:


cd your_study_group_data

setenv SUBJECTS_DIR $PWD

foreach i (*)

echo $i

recon-all -subjid $i -qcache -measure CBF.mgh

end

mris_preproc ran on the smoothed output files!

Thanks for your help.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Greve, Douglas N.,Ph.D. 

Sent: Thursday, February 21, 2019 9:22 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc error: dimension mismatch

If you have a volume and a registration file, you can run mris_preproc
with the --iv option. Eg, something like

mris_preproc --fsgd abc.fsgd --target fsaverage --hemi lh \

  * --out abc-lh-vol.mgh --iv abc01-func/bold/main/nvr/ces.bhdr
abc01-func/bold/register.lta --iv abc02-func/bold/main/nvr/ces.bhdr
abc02-func/bold/register.lta --iv abc03-func/bold/main/nvr/ces.bhdr
abc03-func/bol/register.lta --iv abc04-func/bold/main/nvr/ces.bhdr
abc04-func/bold/register.lta



On 2/20/19 7:20 PM, Peters, Douglas G wrote:
>
> External Email - Use Caution
>
> Hi Doug,
>
> I'm still trying to troubleshoot my mris_preproc error: dimension
> mismatch.
>
> I don't think qcache was run on the CBF images because they were last
> processed in SPM (working on old dataset made by someone else)...there
> aren't any smooth fwhm files. Is it possible to run qcache on a
> nonnative freesurfer file? i.e. recon-all -s  -qcache -measure
> CBF.mgh?
>
> Since I don't think this is an option I'm trying to run mri_surf2surf
> (--srcsubject subjid --srcsurfval subjid/surf/lh.CBF.fwhm10.mgh (ran
> in to type 3 error when didn't specify the path) --trgsubject
> fsaverage --trgsurfval lh.thickness.fsaverage.mgh --hemi lh should
> I be using a different target file?
>
> Hopefully this will solve my issue.
>
> Also, is it possible that different FS versions create different
> vertices?  I am remaking my fsaverage with an older FS version to see
> if that may fix the issue.
>
> Please let me know if my questions are unclear, and I will try to
> rephrase and add script input/output.
>
> Thanks,
> Doug P
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Friday, February 15, 2019 8:26 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] mris_preproc error: dimension mismatch
> The subject surface probably changed since the last time you ran
> qcache and now has a different number of vertices. Try re-running
> qcache for those subjects.
>
> On 2/15/19 2:58 AM, Peters, Douglas G wrote:
>>
>> External Email - Use Caution
>>
>> Hi Everyone,
>>
>> I'm trying to prepare my Cerebral blood flow surface data for
>> mri_glmfit group analysis (qdec doesn't allow you to choose your own
>> subject surface files to analyze, so I figured mri_glmfit is my only
>> option). Quick summary of what I did and where I get stuck:
>>
>> ##
>>
>> I made a vol2surf conversion for some subject perfusion images hoping
>> to evaluate CBF as if it were cortical thickness.The original CBF
>> volumes were registered and normalized in SPM and saved as CBF.nii
>> all in same T1 space.I made them into surface files using :
>> mri_vol2surf --mov CBF.nii--regheader SubjectID --hemi rh --projfrac
>> 0.5 --fwhm 10 --o CBF.mgh
>>
>>
>> I then tried to run:
>>
>> mris_preproc --fsgd CBF.fsdg \
>>
>> --cache-in CBF.fwhm10 \
>>
>> --target fsaverage \
>>
>> --hemi rh \
>>
>> --out rh.CBF.10.mgh\
>>
>>
>> scans through all the subject .mghs
>>
>> ninputs = # subjects
>>
>> Checking inputs
>>
>>
>> "ERROR: dimension mismatch between" the first two surface files in my
>> subject fsdg file
>>
>>
>> ##
>>
>>
>> Please help. What should I do to get around this?
>>
>>
>> Thanks,
>>
>> DP
>>
>>
>>
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>
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[Freesurfer] recon-all -hires

2019-02-21 Thread Nasiriavanaki, Zahra 
Dear Freesurfer experts


I was running recon-all command with hires flag for our high resolution fMRI 
data, but it has been in a constant status since yesterday.

I copied the last few lines that are currently in my terminal. I had the same 
issue with another subject before, and I had to terminate the recon-all and run 
it without -hires.

Could you please let me know how I can solve this issue?


Thanks

Mona



#@# Fix Topology Copy rh Wed Feb 20 19:50:00 EST 2019
/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/scripts

 cp ../surf/rh.orig.nofix ../surf/rh.orig


 cp ../surf/rh.inflated.nofix ../surf/rh.inflated

#@# Fix Topology lh Wed Feb 20 19:50:03 EST 2019

 mris_fix_topology -rusage 
/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.lh.dat
 -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T lh

#@# Fix Topology rh Wed Feb 20 19:50:03 EST 2019

 mris_fix_topology -rusage 
/autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR/inul_loom2_7T/touch/rusage.mris_fix_topology.rh.dat
 -mgz -sphere qsphere.nofix -ga -seed 1234 inul_loom2_7T rh

Waiting for PID 8994 of (8994 8997) to complete...



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Re: [Freesurfer] mri_convert

2019-02-21 Thread Greve, Douglas N.,Ph.D. 



On 2/21/19 12:56 PM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
>
> Thanks for the response.
> yes, I need to extract the acquisition times for kinetic modeling 
> using PET surfer. Please I have two follow-up questions and I 
> appreciate any highlights:
> - Are the acquisition times that PET surfer needs to be included in a 
> file called time.dat can be extracted from the PET DICOM header - tag 
> (0008 ,0013) which labeled "Instance Creation Time" is this the 
> correct tag?
I don't know what tags you need to extract the right numbers. Probably 
not the instance creation time.
> - intensity scaling is not imbedded in the dicom, do you kindly 
> suggest how I can convert the PET DICOMS to nifti?
You can use this version of mri_convert
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_convert
>
> Thanks so much!
> John
>
>
>
>
> you mean you want the acquisition times to do kinetic modeling? I 
> don't have anything to do that. Also, you should check to see whether 
> your PET has intensity scaling imbedded in the dicom as the v6 
> mri_convert does not handle this properly.
>
>
> On 2/20/19 11:44 AM, john Anderson wrote:
>
> >
>
> > External Email - Use Caution
>
> >
>
> > hi FS experts.
>
> > I would like to inquire about the command mri_ convert I use this
>
> > command to convert fMRI and PET 4D volumes from dicom format to nifti.
>
> >
>
> > Are there any flags that can be used in mri_convert command line to
>
> > enable it to extract a text file contain each series time in seconds?
>
> >
>
> > thanks
>
> > John
>
> >
>
> >
>
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>
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Re: [Freesurfer] mri_convert

2019-02-21 Thread john Anderson 
External Email - Use Caution

Hi Dr Greve,

Thanks for the response.
yes, I need to extract the acquisition times for kinetic modeling using PET 
surfer. Please I have two follow-up questions and I appreciate any highlights:
- Are the acquisition times that PET surfer needs to be included in a file 
called time.dat can be extracted from the PET DICOM header - tag (0008 ,0013) 
which labeled "Instance Creation Time" is this the correct tag?
- intensity scaling is not imbedded in the dicom, do you kindly suggest how I 
can convert the PET DICOMS to nifti?

Thanks so much!
John

you mean you want the acquisition times to do kinetic modeling? I don't have 
anything to do that. Also, you should check to see whether your PET has 
intensity scaling imbedded in the dicom as the v6 mri_convert does not handle 
this properly.

On 2/20/19 11:44 AM, john Anderson wrote:

>

> External Email - Use Caution

>

> hi FS experts.

> I would like to inquire about the command mri_ convert I use this

> command to convert fMRI and PET 4D volumes from dicom format to nifti.

>

> Are there any flags that can be used in mri_convert command line to

> enable it to extract a text file contain each series time in seconds?

>

> thanks

> John

>

>

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Re: [Freesurfer] Extracting anatomical locations for a set of RAS coordinates

2019-02-21 Thread Greve, Douglas N.,Ph.D. 
For a volume, I would do it differently. In matlab

[segcodes segnames ] = read_fscolorlut(); % read in the seg lookup table

aparcaseg = MRIread('aparc+aseg.mgz'); % Load in the volume
crs = round(inv(aparcaseg.tkrvox2ras)*[tkr tka tks 1]')+1; % convert 
your tkreg coords to col, row, and slice
c = crs(1);
r = crs(2);
s = crs(3);
segno = aparcaseg.vol(r,c,s); % extract the segmentation number
ind = find(segno == segcodes); % convert to the ne name of the segmentation
segname = segnames(ind,:)


On 2/20/19 9:58 AM, Sparsh Jain wrote:
>
> External Email - Use Caution
>
> Hi Doug,
>
> I tried what you suggested, but it did not work (see below for details 
> of what we tried). We have TkReg RAS coordinates (or vertex points) 
> for our electrode contacts; most contacts are _deep within the 
> brain_ (e.g., hippocampus and amygdala). We want to get a variable in 
> Matlab that will give us the anatomical labels as a function of the 
> TkReg RAS coordinates (or vertex points). How can we do this?
>
> Thanks!
>
> Sparsh
>
> _What I tried:_ I read the 'rh.aparc.2009a.annot' file in matlab using 
> read_annotation.m. That gave me 76 labels for right hemisphere, which 
> I believe correspond to the surface parcellations only. In freeview I 
> loaded the orig.mgz, aparc.a2009s+aseg.mgz, rh.pial and rh.inflated. I 
> then clicked on a cortical surface point to see if I can get the 
> corresponding vertex number or structure ID. On doing so, I found a 
> value in the Vertex row under rh.pial of freeview but this number 
> wasn't found in the matlab output (in the colortable.label or 
> colortable.table). I think I am looking in the wrong place to find the 
> vertex # on freeview.
>
> Also, I did not find a readable file for the segmentation data. I 
> tried to read the aparc.a2009s+aseg.mgz on Matlab but that didn't work.
> Show quoted text
>
> On Thu, 7 Feb 2019, 16:10 Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu> wrote:
>
> First, you'll have to find the closest vertex for each point in
> fsavarage. You can do this with by creating a label file then using
> mri_label2label with the --paint option.
>
> To find the label associated with each vertex, it is  probably
> easiest
> to use matlab using read_surf.m and read_annotation.m
>
> On 2/5/19 11:17 AM, Sparsh Jain wrote:
> >
> > External Email - Use Caution
> >
> > Good afternoon
> >
> > Is there is way to automatically extract the anatomical locations
> > corresponding to a set of RAS coordinates using Freesurfer's
> atlas? I
> > have a set of 200 points and I am trying to get their anatomical
> > labels automatically.
> >
> > Thank you
> > Sparsh
> >
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>
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Re: [Freesurfer] Sections of Temporal Lobe not included

2019-02-21 Thread Greve, Douglas N.,Ph.D. 
Is there a defect in those regions? 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview 


On 2/20/19 9:33 AM, John Mc Fadden wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
> Here are the rotated images
>
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Greve, 
> Douglas N.,Ph.D.
> Sent: 14 February 2019 16:36
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Sections of Temporal Lobe not included
>
> hard to tell from those images what is happening. Can you send an image
>
> with an arrow pointing to where the problem is? Putting the brain
>
> right-side-up will be helpful as well
>
> On 2/14/19 8:12 AM, John Mc Fadden wrote:
>
> >
>
> > External Email - Use Caution
>
> >
>
> > Hi,
>
> >
>
> > I have processed two subjects data twice, once using T1w only and once
>
> > including FLAIR. I haven’t been able to achieve good coverage of the
>
> > temporal lobe (see images) with either method for one patient,
>
> > slightly better performance with the other. Is there anything else I
>
> > could do to avoid manual segmentation? Thanks for any help.
>
> >
>
> > All the best
>
> >
>
> > John
>
> >
>
> >
>
> > ___
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> > Freesurfer mailing list
>
> > Freesurfer@nmr.mgh.harvard.edu
>
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Re: [Freesurfer] CAT12 surfaces on tkregister2 and Freeview

2019-02-21 Thread Greve, Douglas N.,Ph.D. 
When you run mris_convert try adding --vol-geom orig.mgz where orig.mgz

On 2/20/19 7:14 AM, Loucao, Ricardo wrote:
>
> External Email - Use Caution
>
> Dear FS experts and users,
>
> I’m having some troubles with CAT surfaces visualisation in 
> tkregister2 and Freeview.
>
> Context: I’ve generated some surfaces with CAT12 and I’ve double 
> checked them with Freeview [see attachment1]. Since they looked 
> reasonable, I wanted to project some quantitative MRI data onto the 
> surface, for visualisation purposes only. I used bbregister to 
> register the qMRI brain to the anatomy brain and I’ve checked the 
> results with Freeview, which seemed quite good. Finally, I used 
> mri_vol2surf to get the projection I wanted onto the CAT surface.
>
> My problem is when I add the surface overlay the results seem very 
> off, as if the surface from which the overlay is derived is not in the 
> proper space. When I check the registration using tkregister2 I 
> discovered the source of the problem [see attachment2]. It seems to me 
> like the CAT surface is loaded into tkregister2 with a different 
> transform than in Freeview, and, I guess, mri_vol2surf is doing the 
> same as tkregister2.
>
> My question is: is there any way to force mri_vol2surf to load the 
> surfaces like Freeview does? Any help is highly appreciated!
>
> Here’s a rundown of the commands I ran after the CAT12 .gii file is 
> created:
> mris_convert ?h.CATsurface.gii ?h.central
> bbregister --s $subjid --mov qMRImap.nii --init-fsl --reg register.dat 
> --t2
> mri_vol2surf --mov qMRImap.nii --ref orig.mgz --reg register.dat 
> --hemi ?h --surf central --o qMRIsurf.mgz
>
> Thank you very much in advance!
>
> Ricardo
>
>
>
> 
> 
> Forschungszentrum Juelich GmbH
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> 
>
>
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Re: [Freesurfer] registration and resampling in native space

2019-02-21 Thread Greve, Douglas N.,Ph.D. 
Yes,  if you run it with the --targ as orig.mgz for the given subject, 
then it will sample each run into the anatomical space (this can create 
enourmous data data files!). Alternatively, you can run preproc-sess 
with the --per-session flag and it will align all the runs to a single 
template but otherwise keep everything in the functional space

On 2/20/19 11:53 AM, Francesca Strappini wrote:
>
> External Email - Use Caution
>
> I'll try to find some visual way to show what I mean, but it's really 
> something mild and probably negligible.
> Do you know if is it possible with mri_vol2vol to give to all the runs 
> that belong to the same subject the same system coordinates? So that 
> each voxel across runs will have the same coordinates. I noticed that 
> the transformation matrix is written in the header but it's not really 
> applied to the data. Thank you!
>
>
> Best
> Francesca
>
>
> On Mon, Feb 18, 2019, 12:57 AM Bruce Fischl 
> mailto:fis...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Francesca
>
> can you send us an image that shows why you think it can be improved?
>
> cheers
> Bruce
> On
> Mon, 18 Feb 2019, Francesca Strappini wrote:
>
> >
> > External Email - Use Caution
> >
> > Thank you!Now the registration is better but still not perfect.
> Is there a way to improve it?
> >
> > Best
> >
> > Il giorno gio 14 feb 2019 alle ore 23:30 Greve, Douglas N.,Ph.D.
> mailto:dgr...@mgh.harvard.edu>> ha
> > scritto:
> >       Is func_data.nii.gz an fMRI scan? If so, wouldn't be T2
> weighted? If so,
> >       you should use --t2 instead of --t1 in bbregister
> >
> >       On 2/14/19 2:18 PM, Francesca Strappini wrote:
> >       >
> >       > External Email - Use Caution
> >       >
> >       > Hi Doug,
> >       >
> >       > Could you advise me about how to correctly run mri_vol2vol?
> >       > The functional data did not get perfectly registered to
> the anatomy so
> >       > I'm afraid I'm not running it correctly.
> >       >
> >       > Thanks!
> >       >
> >       >
> >       > Il giorno mar 12 feb 2019 alle ore 17:21 Bruce Fischl
> >       >  
>  >> ha
> >       > scritto:
> >       >
> >       >     Hi Francesca
> >       >
> >       >     sorry, I defer to Doug on the details of mri_vol2vol.
> >       >
> >       >     cheers
> >       >     Bruce
> >       >
> >       >     On Tue, 12 Feb 2019,
> >       >     Francesca Strappini wrote:
> >       >
> >       >     >
> >       >     > External Email - Use Caution
> >       >     >
> >       >     > Thank you for the reply!
> >       >     > I run:
> >       >     > mri_vol2vol --reg register.dat --mov
> func_data.nii.gz --targ
> >       >     > /usr/local/freesurfer/subjects/sub3/mri/T1.mgz --o
> >       >     func_data_registered2T1.nii.gz --no-resample
> >       >     >
> >       >     > Then I checked the registration and it seems that
> the original
> >       >     run is better aligned to the T1 than
> >       >     > the registered one. Maybe am I not running
> mri_vol2vol correctly?
> >       >     >
> >       >     > Thanks!
> >       >     > Best
> >       >     >
> >       >     >
> >       >     > Il giorno mar 12 feb 2019 alle ore 02:19 Bruce Fischl
> >       >      
>  >>
> >       >     ha scritto:
> >       >     >       Hi Francesca
> >       >     >
> >       >     >       check out the --no-resample option in
> mri_vol2vol. It just
> >       >     changes the
> >       >     >       header, so I think should do what you want.
> >       >     >
> >       >     >       cheers
> >       >     >       Bruce
> >       >     >
> >       >     >
> >       >     >       On Tue, 12 Feb 2019, Francesca Strappini wrote:
> >       >     >
> >       >     >       >
> >       >     >       > External Email - Use Caution
> >       >     >       >
> >       >     >       > Dear Freesurfer's experts,
> >       >     >       >
> >       >     >       > I would like to register some functional
> data to the T1,
> >       >     that were collected in
> >       >     >       separate days.
> >       >     >       > I used bbregister:
> >       >     >       >
> >       >     >       > bbregister --s sub3 --mov func_data.nii.gz
> - --reg
> >       >     register.dat --init-coreg --t1
> >       >     >       >
> >       >     >       > Now, I would like to resample the data
> based

Re: [Freesurfer] mri_convert

2019-02-21 Thread Greve, Douglas N.,Ph.D. 
you mean you want the acquisition times to do kinetic modeling? I don't 
have anything to do that. Also, you should check to see whether your PET 
has intensity scaling imbedded in the dicom as the v6 mri_convert does 
not handle this properly.

On 2/20/19 11:44 AM, john Anderson wrote:
>
> External Email - Use Caution
>
> hi FS experts.
> I would like to inquire about the command mri_ convert
> I use this command to convert fMRI and PET 4D volumes from dicom 
> format to nifti.
>
> Are there any flags that can be used in mri_convert command line to 
> enable it to extract a text file contain each series time in seconds?
>
> thanks
> John
>
>
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Re: [Freesurfer] Fw: clusters annotation file in surface - ERROR

2019-02-21 Thread Greve, Douglas N.,Ph.D. 
what happens if you load it into freeview instead of tksurfer?
How did you create lh.surf_combined-magn_CL_fwhm1.mgh ? Does it look ok 
on the surface? Are the values integers?


On 2/20/19 12:56 PM, Barletta, Valeria wrote:
> Thank you Doug,
> As you suggested, I tried to use that command
> (mris_seg2annot --seg lh.surf_combined-magn_CL_fwhm1.mgh --s 
> MS072_R01_04 --hemi lh --ctab MS072_R01_04.txt --o lh.cortical_les.annot)
> but I got this error on tksurfer:
> Successfully parsed tksurfer.tcl
> reading white matter vertex locations...
> % reading colortable from annotation file...
> colortable with 7 entries read (originally MS072_R01_04.txt)
> Found embedded color table in annotation.
> 131940 vertices did not have an annotation!
> surfer: WARNING: no labels imported; annotation was empty
> I attach my color table file...
> Thanks for your help,
> Vale
> ___
> *>Greve, Douglas N.,Ph.D.*DGREVE at mgh.harvard.edu   
> 
> />Tue Feb 19 16:33:32 EST 2019/
> >You can create an annotation with mris_seg2annot (you basically have a 
> >surface-based segmentation). Run it with --help to get more info 
> >including examples. You will need to create your own color table
>
> On 2/19/19 3:21 PM, Barletta, Valeria wrote:
> >//>/Dear Freesurfers, />//>/I have a 3D volume mask of cortical lesions with 
> >8 different clusters />/(8 cortical lesions). />//>/I projected this mask to 
> >the cortex and obtained a .mgh file with the />/command vol2surf: 
> >/>//>/mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out 
> >/>/$path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" 
> >/>/--projfrac-avg -0.1 1 0.05 --hemi $hemi --regheader $subj />//>//>/Now I 
> >need to extract label files from this surface file, one />/label for each 
> >cluster, and then an annotation file summarizing all />/the label files. 
> >/>//>/How can I do this? />//>/Thanks, />//>/Vale/
>
>
>
> 
> *From:* Barletta, Valeria
> *Sent:* Tuesday, February 19, 2019 3:21 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* clusters annotation file in surface
>
> Dear Freesurfers,
>
> I have a 3D volume mask of cortical lesions with 8 different clusters 
> (8 cortical lesions).
>
> I projected this mask to the cortex and obtained a .mgh file with the 
> command vol2surf:
>
> mri_vol2surf --src $path_to_lesion/$subj/combined-$lesion.nii.gz --out 
> $path_to_output/$subj/surf/$hemi".surf_combined-"$lesion".mgh" 
> --projfrac-avg -0.1 1 0.05 --hemi $hemi --regheader $subj
>
>
> Now I need to extract label files from this surface file, one 
> label for each cluster, and then an annotation file summarizing all 
> the label files.
>
> How can I do this?
>
> Thanks,
>
> Vale
>
>
>
>
>
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Re: [Freesurfer] mris_preproc error: dimension mismatch

2019-02-21 Thread Greve, Douglas N.,Ph.D. 
If you have a volume and a registration file, you can run mris_preproc 
with the --iv option. Eg, something like

mris_preproc --fsgd abc.fsgd --target fsaverage --hemi lh \

  * --out abc-lh-vol.mgh --iv abc01-func/bold/main/nvr/ces.bhdr
abc01-func/bold/register.lta --iv abc02-func/bold/main/nvr/ces.bhdr
abc02-func/bold/register.lta --iv abc03-func/bold/main/nvr/ces.bhdr
abc03-func/bol/register.lta --iv abc04-func/bold/main/nvr/ces.bhdr
abc04-func/bold/register.lta



On 2/20/19 7:20 PM, Peters, Douglas G wrote:
>
> External Email - Use Caution
>
> Hi Doug,
>
> I'm still trying to troubleshoot my mris_preproc error: dimension 
> mismatch.
>
> I don't think qcache was run on the CBF images because they were last 
> processed in SPM (working on old dataset made by someone else)...there 
> aren't any smooth fwhm files. Is it possible to run qcache on a 
> nonnative freesurfer file? i.e. recon-all -s  -qcache -measure 
> CBF.mgh?
>
> Since I don't think this is an option I'm trying to run mri_surf2surf 
> (--srcsubject subjid --srcsurfval subjid/surf/lh.CBF.fwhm10.mgh (ran 
> in to type 3 error when didn't specify the path) --trgsubject 
> fsaverage --trgsurfval lh.thickness.fsaverage.mgh --hemi lh should 
> I be using a different target file?
>
> Hopefully this will solve my issue.
>
> Also, is it possible that different FS versions create different 
> vertices?  I am remaking my fsaverage with an older FS version to see 
> if that may fix the issue.
>
> Please let me know if my questions are unclear, and I will try to 
> rephrase and add script input/output.
>
> Thanks,
> Doug P
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Friday, February 15, 2019 8:26 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] mris_preproc error: dimension mismatch
> The subject surface probably changed since the last time you ran 
> qcache and now has a different number of vertices. Try re-running 
> qcache for those subjects.
>
> On 2/15/19 2:58 AM, Peters, Douglas G wrote:
>>
>> External Email - Use Caution
>>
>> Hi Everyone,
>>
>> I'm trying to prepare my Cerebral blood flow surface data for 
>> mri_glmfit group analysis (qdec doesn't allow you to choose your own 
>> subject surface files to analyze, so I figured mri_glmfit is my only 
>> option). Quick summary of what I did and where I get stuck:
>>
>> ##
>>
>> I made a vol2surf conversion for some subject perfusion images hoping 
>> to evaluate CBF as if it were cortical thickness.The original CBF 
>> volumes were registered and normalized in SPM and saved as CBF.nii 
>> all in same T1 space.I made them into surface files using : 
>> mri_vol2surf --mov CBF.nii--regheader SubjectID --hemi rh --projfrac 
>> 0.5 --fwhm 10 --o CBF.mgh
>>
>>
>> I then tried to run:
>>
>> mris_preproc --fsgd CBF.fsdg \
>>
>> --cache-in CBF.fwhm10 \
>>
>> --target fsaverage \
>>
>> --hemi rh \
>>
>> --out rh.CBF.10.mgh\
>>
>>
>> scans through all the subject .mghs
>>
>> ninputs = # subjects
>>
>> Checking inputs
>>
>>
>> "ERROR: dimension mismatch between" the first two surface files in my 
>> subject fsdg file
>>
>>
>> ##
>>
>>
>> Please help. What should I do to get around this?
>>
>>
>> Thanks,
>>
>> DP
>>
>>
>>
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>
>
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Re: [Freesurfer] White matter volume from aseg

2019-02-21 Thread Greve, Douglas N.,Ph.D. 
It is cerebral white matter, so it excludes brainstem and cerebellar white

On 2/21/19 11:14 AM, Mehndiratta, Ambica wrote:
> Hello,
>
> I am trying to extract the white matter volume based off the 
> aseg.stats. I noticed the text includes "total cortical white matter 
> volume" and I was wondering if that is the same as overall white 
> matter volume in the brain?
>
> Thank you,
>
> Ambica Mehndiratta
> Clinical Research Coordinator
> Massachusetts General Hospital
> 149 13th Street, Charlestown MA 02129
> amehndirat...@mgh.harvard.edu
> (617)-724-8823
>
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Re: [Freesurfer] Special image protocol

2019-02-21 Thread Greve, Douglas N.,Ph.D. 
I highly recommend the multiecho mprage at about 1mm.

On 2/21/19 10:30 AM, Bruce Fischl wrote:
> Hi Mustafa
>
> FreeSurfer should work fine with many image protocols. If you have the
> freedom to choose one, Andre van der Kouwe (ccd) can point you at the
> sequence he developed for Siemens. If you are using a different scanner
> give us the details and we can recommend something
>
> cheers
> Bruce
>
>
> On Thu, 21 Feb
> 2019, mustafa amin wrote:
>
>> External Email - Use Caution
>>
>> Dear member,
>>
>> I am really new with this freesurfer, just need to ask 1 question. Is there 
>> a special image protocol before running the MRI and then upload it to 
>> freesurfer? Please share your thoughts. Thank you for your kind attention 
>> and cooperation.
>>
>> Yours faithfully,
>>
>> Mustafa M. Amin
>> Consultant Psychiatrist in Biological Psychiatry
>> Department of Psychiatry
>> Faculty of Medicine
>> Universitas Sumatera Utara
>>
>>
>> ___
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>>
>>
>>
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[Freesurfer] White matter volume from aseg

2019-02-21 Thread Mehndiratta, Ambica 
Hello,

I am trying to extract the white matter volume based off the aseg.stats. I 
noticed the text includes "total cortical white matter volume" and I was 
wondering if that is the same as overall white matter volume in the brain?

Thank you,

Ambica Mehndiratta
Clinical Research Coordinator
Massachusetts General Hospital
149 13th Street, Charlestown MA 02129
amehndirat...@mgh.harvard.edu
(617)-724-8823
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Re: [Freesurfer] Special image protocol

2019-02-21 Thread Bruce Fischl 
Hi Mustafa

FreeSurfer should work fine with many image protocols. If you have the 
freedom to choose one, Andre van der Kouwe (ccd) can point you at the 
sequence he developed for Siemens. If you are using a different scanner 
give us the details and we can recommend something

cheers
Bruce


On Thu, 21 Feb 
2019, mustafa amin wrote:

>External Email - Use Caution
>
> Dear member,
>
> I am really new with this freesurfer, just need to ask 1 question. Is there a 
> special image protocol before running the MRI and then upload it to 
> freesurfer? Please share your thoughts. Thank you for your kind attention and 
> cooperation.
>
> Yours faithfully,
>
> Mustafa M. Amin
> Consultant Psychiatrist in Biological Psychiatry
> Department of Psychiatry
> Faculty of Medicine
> Universitas Sumatera Utara
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] segmentation error

2019-02-21 Thread mara alves 
External Email - Use Caution

Hi there,

Just want to check if you get the recon-all files that I sent for an entire
subject?!

I am also wondering if the problem with the segmentation can be related to
the small size of aged Portuguese brains considering the expected size
based for instance on the MNI space?!

Because pial segmentation is including intensities under 110 and the aseg
maps are also badly estimated

Em quarta-feira, 20 de fevereiro de 2019, Bruce Fischl <
fis...@nmr.mgh.harvard.edu> escreveu:

> hmmm, I don't see anything glairing in the log. I guess upload the subject
> and we'll take a look
> Bruce
>
>
> On Wed, 20 Feb 2019, mara alves wrote:
>
>
>> External Email - Use Caution
>>
>> Here is the recon-all.log for one for old subjects.Thanks,
>> Mara
>>
>> mara alves  escreveu no dia quarta, 20/02/2019
>> à(s) 09:57:
>>   Hi,
>> Thanks for the quick reply. What do you mean about uploading the entire
>> subject? All the
>> output files of the recon -all?
>>
>> Best,
>> Mara
>>
>> Bruce Fischl  escreveu no dia terça,
>> 19/02/2019 à(s) 23:10:
>>   wow, that looks pretty bad. Can you send us the recon-all.log (or
>> upload
>>   the entire subject and we will investigate)?
>>   On Tue, 19 Feb 2019, mara alves
>>   wrote:
>>
>>   >
>>   > External Email - Use Caution
>>   >
>>   > Hi there,
>>   >
>>   > I ran the recon -all command in two samples, one of young
>> participants and
>>   another of older
>>   > subjects.
>>   >
>>   > The segmentation worked well for young participants, however it
>> seems that for
>>   older participants
>>   > the white.pial segmentation it is being done incorrectly. I
>> believe it is
>>   segmenting the gray matter
>>   > instead (please see the pics attached).
>>   >
>>   > Best,
>>   > Mara
>>   >
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>>
>>
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