date:20160413

[Freesurfer] Different significant clusters: qdec vs mri_glmfit-sim

2016-04-13 Thread Cassandra Wannan

Hi Freesurfer experts,

Qdec does not appear to allow me to automatically extract mean values for
significant clusters for each participant, so I have been doing this using
command line after running the original analysis in Qdec. However, I have
found that there are some differences in the significant clusters between
the two. The command line I am using is:

mri_glmfit-sim --glmdir TRSCtrl_Vocab_DODS --cache 2 abs --cwp 0.01

I believe that this should correspond to analysis in Qdec using the preset
threshold of 2 and Monte-Carlo Null-Z Simulation value of 2.0 (0.01).

The significant clusters from Qdec are:

# ClusterNo  Max   VtxMax   Size(mm^2)  TalX   TalY   TalZCWP
CWPLowCWPHi   NVtxs   Annot

   17.740  109023669.23 -6.1  -12.5   47.0  0.00120
0.00080  0.00170  1618  paracentral

   25.854   63055   1542.69-19.0  -73.2   -3.6  0.00010
0.0  0.00020  1913  lingual

   35.393  127437   1063.38-23.4   -6.9  -28.0  0.00010
0.0  0.00020  2069  entorhinal

   45.026  112833788.05-13.9  -45.3   38.9  0.00010
0.0  0.00020  1660  precuneus

   54.726  141529523.23-34.4   -5.7   10.9  0.00760
0.00650  0.00870  1456  insula

   64.413   23898863.24-13.4   25.1   26.4  0.00010
0.0  0.00020  1495  superiorfrontal

   73.819   21492874.38-17.8  -72.7   29.0  0.00010
0.0  0.00020  1321  precuneus

Whereas from the command line:

# ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWP
CWPLowCWPHi   NVtxs   Annot

   17.740  109023668.36 56.9  -11.3   35.0  0.00050
0.00020  0.00080  1618  postcentral

   25.854   63055   1328.30 52.2  -58.3   -8.8  0.00010
0.0  0.00020  1913  inferiortemporal

   35.393  127437   1004.26 32.5   -2.8  -38.4  0.00010
0.0  0.00020  1950  fusiform

   45.026  112833782.44 54.3  -41.2   42.3  0.00010
0.0  0.00020  1660  supramarginal

   54.413   23898780.09 56.52.16.1  0.00010
0.0  0.00020  1495  precentral

   63.819   21492673.28 46.3  -59.1   31.8  0.00050
0.00020  0.00080  1321  inferiorparietal

When I view the glmfit clusters in free view they do appear very similar to
the ones in Qdec, but there is one less significant clusters and obviously
the cluster names are different. Am I using the correct command line to
extract this information?

Many thanks,

Cassie
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[Freesurfer] FSFAST (seed based correlation analysis)

2016-04-13 Thread Alshikho, Mohamad J.

Hi Freesurfers,
How can I perform seed based correlation analysis using PET images? In other 
words how can I use the same approach of FSFAST, but by including PET images 
instead of fmri images, to study the correlation between PET signal within  a 
seed mask ( e.g precentral gyrus ) and the whole brain regions?

What is the best approach to run this analysis?


Best,
Mohamad
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Re: [Freesurfer] missing baseline in longitudinal analysis

2016-04-13 Thread Martin Reuter

Just leave out that row (second case)
Best Martin
On Apr 13, 2016 8:30 AM, Mihaela Stefan wrote:Hi Martin!
Sorry to bug you but I have one more question. How do I create the Qdec table without the baseline for that subject? Do I leave the baseline time point out or I still enter it in the table?
For example
fsid fsid-base years
Study1_Subj1_MRI0. Study1_Subj1. 0
Study1_Subj1_MRI1. Study1_Subj1. 1.25
Study1_Subj1_MRI2. Study1_Subj1. 2.25
OR
Study1_Subj1_MRI1. Study1_Subj1. 1.25
Study1_Subj1_MRI2. Study1_Subj1. 2.25
Thanks!
Mihaela
On Apr 12, 2016 7:13 PM, "Martin Reuter" wrote:It does not compute this. Often people use time-from-baseline for their analysis and control for age (@ baseline).
Best Martin
On Apr 12, 2016 6:23 PM, Mihaela Stefan wrote:Thanks Martin!
Related to the longitudinal analysis, should we use the demeaned age at baseline or the LME package automatically computes this?
Thanks again!
Mihaela
On Apr 12, 2016 5:39 PM, "Martin Reuter" wrote:Hi Michael,
the longitudinal image processing pipeline does not care which one is baseline and which are follow ups. It only cares what images belong to the same subject.
So, yes you can process this one with only two tone points instead of three.
Best Martin
On Apr 12, 2016 5:09 PM, Mihaela Stefan wrote:Hello FreeSurfers,We are conducting a longitudinal analysis and we have a subject who is missing the structural at baseline (it has fMRI data though). That subject returned for the 1st and the 2nd follow-up. Can we process the longitudinal pipeline the usual way and account for the missing baseline in the LME analysis? The other option would be to treat the 1st follow-up as baseline but we would like to be consistent with the fMRI analyses and keep the baseline time point.Thanks!Mihaela
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Re: [Freesurfer] glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)

2016-04-13 Thread Pedro Rosa

Thanks, Doug.
When I do it, I get the following error: ERROR: must spec --sim
I am using FreeSurfer 5.3 in a Mac OS. I read in the wiki that mri_mcsim
got an atualization for Linux. Should I get that atualization for Mac Os?
Best,
Pedro.

On Wed, Apr 13, 2016 at 11:43 AM, Douglas Greve 
wrote:

> Try it without the --no-sim. The --no-sim was from before I stored the
> cached data and you either had to run a simulation or not.
>
>
> On 4/12/16 9:10 PM, Pedro Rosa wrote:
>
> Dear list,
> I want to limit my vertex-wise group analysis to a smaller spatial region,
> then I ran my own Monte-Carlo simulation on fsaverage for the superior
> temporal gyrus:
>
> mri_mcsim --o lh/superiortemporal --base mc-z --surface /fsaverage lh
> --nreps 1 --label superiortemporal
>
>
> After 36 hours, it finished and I pasted the resulting into 
> $FREESURFER_HOME/average/mult-comp-cor/fsaverage, and
> ran glmfit:
>
> mri_glmfit --glmdir glmdir --y lh.thickness.5.mgh --fsgd table.fsgd --C
> contrast.mtx --surface fsaverage lh --label
> /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label
>
> It seems it ran only on the label, as expected.
>
> However I am not able touse this pre-cached simulation in mri_glmfit-sim.
>
> I tried: mri_glmfit-sim --glmdir glmdir --sim-sign abs --cache-dir
> $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/superiortemporal
> --no-sim mc-z.abs.th13 --cache-label
> /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label
>
>
> ...but I get an error although the csd files are in
> /average/mult-comp-cor/fsaverage... path : ERROR: cannot find any csd
> files
>
> I tried several combinations of the text specified after --no-sim, but all
> I got is the error above. I though I should refer to my own simulation
> using --cache-dir, but it requires the --no-sim flag.
>
> Can anyone help me?
>
> Best,
>
> Pedro Rosa.
>
>
>
>
>
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Re: [Freesurfer] Freesurfer v6 beta

2016-04-13 Thread Eugenio Iglesias

Hi again, 
in the paper, we used FreeSurfer 5.3 the process the data (recon-all), and then 
run the hippocampal module on top of that. So, with a bit of trouble, you can 
reproduce the results.. 
However, the 6.0 beta was taken down, so reproducing the results of the 
recon-all stream would be hard, and since such results affect the hippocampal 
module, reproducing the subfield segmentation would in turn also be hard. 
Does this make sense? 
Cheers, 
/E 

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

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


From: "Francis Tyson Thomas"  
To: "Freesurfer support list"  
Sent: Thursday, April 14, 2016 1:04:31 AM 
Subject: Re: [Freesurfer] Freesurfer v6 beta 

Hi Eugenio, 
I understood this part that you mentioned but I didn't understand how is is 
affected and what would be its consequences? Because I am referring to your 
preprint paper that makes use of v6, so will the results/validity of that paper 
also get affected by these differences. Because in my work the accuracy of the 
segmentation outputs are critical both for analysis and speeding it up. 

Thanks, 
Tyson 

On Wed, Apr 13, 2016 at 3:52 PM, Eugenio Iglesias < e.igles...@bcbl.eu > wrote: 



Hi Tyson, 
the hippocampal module shouldn't change between your beta and the FS6 release, 
but the main recon-all stream will. Since the latter is used to initialize the 
former, the results will be a bit different. 
Cheers, 
/Eugenio 

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

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


From: "Francis Tyson Thomas" < francisttho...@email.arizona.edu > 
To: "Freesurfer support list" < freesurfer@nmr.mgh.harvard.edu > 
Sent: Wednesday, April 13, 2016 8:19:18 PM 
Subject: [Freesurfer] Freesurfer v6 beta 

Hi, 

I was wondering when would the new Freesurfer v6 beta be available? Also I have 
been using the old beta for my hippocampal segmentation and I wanted to know if 
this new beta will affect the results of that? 

Thanks, 
Tyson 

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Re: [Freesurfer] Freesurfer v6 beta

2016-04-13 Thread Francis Tyson Thomas

Hi Eugenio,

I understood this part that you mentioned but I didn't understand how is is
affected and what would be its consequences? Because I am referring to your
preprint paper that makes use of v6, so will the results/validity of that
paper also get affected by these differences. Because in my work the
accuracy of the segmentation outputs are critical both for analysis and
speeding it up.

Thanks,
Tyson

On Wed, Apr 13, 2016 at 3:52 PM, Eugenio Iglesias 
wrote:

> Hi Tyson,
> the hippocampal module shouldn't change between your beta and the FS6
> release, but the main recon-all stream will. Since the latter is used to
> initialize the former, the results will be a bit different.
> Cheers,
> /Eugenio
>
> Juan Eugenio Iglesias
> Postdoctoral researcher BCBL
> www.jeiglesias.com
> www.bcbl.eu
>
> Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
>
> --
> *From: *"Francis Tyson Thomas" 
> *To: *"Freesurfer support list" 
> *Sent: *Wednesday, April 13, 2016 8:19:18 PM
> *Subject: *[Freesurfer] Freesurfer v6 beta
>
> Hi,
>
> I was wondering when would the new Freesurfer v6 beta be available? Also I
> have been using the old beta for my hippocampal segmentation and I wanted
> to know if this new beta will affect the results of that?
>
> Thanks,
> Tyson
>
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Re: [Freesurfer] Freesurfer v6 beta

2016-04-13 Thread Eugenio Iglesias

Hi Tyson, 
the hippocampal module shouldn't change between your beta and the FS6 release, 
but the main recon-all stream will. Since the latter is used to initialize the 
former, the results will be a bit different. 
Cheers, 
/Eugenio 

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

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


From: "Francis Tyson Thomas"  
To: "Freesurfer support list"  
Sent: Wednesday, April 13, 2016 8:19:18 PM 
Subject: [Freesurfer] Freesurfer v6 beta 

Hi, 

I was wondering when would the new Freesurfer v6 beta be available? Also I have 
been using the old beta for my hippocampal segmentation and I wanted to know if 
this new beta will affect the results of that? 

Thanks, 
Tyson 

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Re: [Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

2016-04-13 Thread Douglas N Greve

what is your tksurfer command line? Can you send all the terminal output 
from tksurfer? Does it work in freeview?

On 04/13/2016 11:20 AM, DeCross, Stephanie N. wrote:
> Hi,
>
> I’m trying to take an ROI in MNI152 volume space and make it into a 
> cortical surface label, for visualization purposes.
>
> With my input being the lh thresholded, binarized MNI152 nii.gz label 
> (when I visualize it, it looks as it should in fslview), I ran:
>
> mri_vol2vol -- mov   -- targ 
> $SUBJECTS_DIR/fsaverage/mri/orig.mgz  -- o   -- 
> regheader  -- talres 2  -- interp nearest
> *
> *
> mri_cor2label -- c   -- id 1  -- l 
>  ./
> *
> *
> My commands above seem to have run fine, but when I open the lh in 
> tksurfer and try to load the new lh label file, the dialogue runs for 
> a little but then errors out:
>
> 12304 unassigned vertices in label - building spatial LUT…
> assigning vertex numbers to label...
> MatrixMultiply: m2 is null!
>
> And then tksurfer closes. I’m not sure what’s going wrong - does 
> anyone have any pointers or troubleshooting methods I can try?
>
> Thanks,
> Stephanie
>
> *Stephanie N. DeCross*
> Clinical Research Coordinator
> Psychiatric Neuroimaging Research Program
> Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> 149 13th Street, Rm 2620A
> Charlestown, MA 02129
> Phone: (617) 724-3283
> Fax: (617) 726-4078
>
>
>
>
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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
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Re: [Freesurfer] mri_vol2surf after recon-all

2016-04-13 Thread Douglas N Greve


this is a known bug. Try this version instead
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg

On 04/13/2016 01:06 PM, Trisanna Sprung-Much wrote:
> Hi Doug
>
> So I tried running mni152reg and had the following error:
>
> mni152reg --s icbm-102_test
>
>
> setenv SUBJECTS_DIR /data-01/trisanna/freesurfer
> cd /home/trisanna
> /usr/local/freesurfer-5.3//bin/mni152reg --s icbm-102_test
>
>
> fslregister --mov 
> /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --s 
> icbm-102_test --reg 
> /data-01/trisanna/freesurfer/icbm-102_test/mri/transforms/reg.mni152.2mm.dat 
> --dof 12
> mkdir: cannot create directory 
> ‘/usr/share/fsl/5.0/data/standard/tmp.fslregister.11061’: Permission 
> denied
>
> I spoke with our IT guy and he says that of course I cannot be writing 
> to fsl/5.0/data. I then did a web search and found that someone else 
> was having this problem
>
> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41276.html
>
> How might I fix this? Let me know if I should send the log file that 
> was created.
>
> best
>
> Trisanna
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Fri, Apr 8, 2016 at 1:33 PM, Douglas N Greve 
> > wrote:
>
> not sure, mni152reg uses $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
>
> You can always just run the following command directly
>
> fslregister --mov icbm.nii.gz --s $subject --reg
> $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12
>   --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta
>
> This will use a linear (12 dof) registration which might not be
> particularly accurate
>
>
> On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote:
> > thanks, Doug. I'll get started on running all brains using
> recon-all.
> >
> > The MNI has several ICBM templates now:
> >
> > ICBM152 linear
> > ICBM152 nonlinear symmetric VI
> > ICBM152 nonlinear 2009
> >
> > Do you know which one mni152reg is using?
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve
> > 
>  >> wrote:
> >
> >
> >
> > On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote:
> > > thanks, Doug. I am still extremely confused, however. *Am
> I meant to
> > > run recon-all first? *I was told in a previous email that I
> > should do
> > > this first, however, I thought that Freesurfer takes the
> volumes and
> > > does a linear registration to MNI305 template, which would
> not work
> > > for my scans that are linearly registered to ICBM152
> nonlinear 2006
> > > template...
> > run recon-all first, otherwise you won't have surfaces.
> recon-all
> > computes the transform matrix to the mni305 but keeps all
> the data in
> > the native anatomical space. I think the ICBM152 is the same
> as the
> > MNI152. Is that right? If so, you can use mni152reg to
> compute the
> > registration to 152 space. If not, then we'll have to workout
> > something
> > else.
> > >
> > > When you have a moment, could you please outline in a step
> by step
> > > manner the steps I should run to take my labels.mnc and my
> volumes
> > > such that I can generate surfaces for those 50 volumes,
> overlay the
> > > labels (for which I thought I was using mri_vol2surf) and
> then edit
> > > those labels to make them more accurate?
> > so you want to transfer the labels from labels.mnc to the
> surfaces of
> > your individual 50 subjects? Start by running recon-all on
> the 50.
> > > *The idea is that I want to generate some sulcal
> probability maps
> > > using surface-based registration, as I can already generate
> > > probability maps using volumetric registration quite easily.*
> > >
> > > many thanks
> > >
> > > Trisanna
> > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve
> > >  
> >
> >  
> >

Re: [Freesurfer] missing baseline in longitudinal analysis

2016-04-13 Thread Mihaela Stefan

Hi Martin,

I am reposting this. Should we include the missing baseline in the qdec
table or leave it out?

Thanks!
Mihaela

On Wed, Apr 13, 2016 at 8:30 AM, Mihaela Stefan 
wrote:

> Hi Martin!
> Sorry to bug you but I have one more question. How do I create the Qdec
> table without the baseline for that subject? Do I leave the baseline time
> point out or I still enter it in the table?
>
> For example
> fsid   fsid-base years
> Study1_Subj1_MRI0.  Study1_Subj1.   0
> Study1_Subj1_MRI1.   Study1_Subj1.   1.25
> Study1_Subj1_MRI2.   Study1_Subj1.   2.25
>
> OR
>
> Study1_Subj1_MRI1.  Study1_Subj1.1.25
> Study1_Subj1_MRI2.   Study1_Subj1.  2.25
>
>Thanks!
> Mihaela
> On Apr 12, 2016 7:13 PM, "Martin Reuter" 
> wrote:
>
>> It does not compute this. Often people use time-from-baseline for their
>> analysis and control for age (@ baseline).
>> Best Martin
>> On Apr 12, 2016 6:23 PM, Mihaela Stefan  wrote:
>>
>> Thanks Martin!
>>
>> Related to the longitudinal analysis, should we use the demeaned age at
>> baseline or the LME package automatically computes this?
>>
>> Thanks again!
>> Mihaela
>> On Apr 12, 2016 5:39 PM, "Martin Reuter" 
>> wrote:
>>
>> Hi Michael,
>> the longitudinal  image processing pipeline does not care which one is
>> baseline and which are follow ups. It only cares what images belong to the
>> same subject.
>> So, yes you can process this one with only two tone points instead of
>> three.
>>
>> Best Martin
>> On Apr 12, 2016 5:09 PM, Mihaela Stefan  wrote:
>>
>> Hello FreeSurfers,
>>
>> We are conducting a longitudinal analysis and we have a subject who is
>> missing the structural at baseline (it has fMRI data though). That subject
>> returned for the 1st and the 2nd follow-up. Can we process the longitudinal
>> pipeline the usual way and account for the missing baseline in the LME
>> analysis?
>>
>> The other option would be to treat the 1st follow-up as baseline but we
>> would like to be consistent with the fMRI analyses and keep the baseline
>> time point.
>>
>> Thanks!
>> Mihaela
>>
>>
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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
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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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>> addressed. If you believe this e-mail was sent to you in error and the
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>> but does not contain patient information, please contact the sender and
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Re: [Freesurfer] Oblique Slice Acquisition

2016-04-13 Thread Harms, Michael

Just an aside: if you acquire oblique (e.g. AC/PC aligned), and don’t want
FS to rotate the volume back into the native scanner space as part of its
“conformation” step, you can edit the s/qform of the NIFTI header to
appear as a non-oblique acquisition.  As Bruce noted, this isn’t a big
deal, although avoiding the rotation in the conformation step does
eliminate a resampling during the conformation step which will blur/smooth
the data to a small degree.

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu

On 4/13/16, 12:34 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Bruce Fischl"  wrote:

Hi Kate

I don't think that will matter. Try running it through from the original
dicoms and see if things seem accurate. That isn't actually an artifact,
it just looks strange because of the slight angle of the view. My guess is
we will handle this fine

cheers
Bruce

On Wed, 13 Apr
2016, Katherine Reiter wrote:

> Hello freesurfer experts,
> I am working with a dataset that was acquired with oblique slices
>aligned to
> each participant's ac-pc line.
>
> 1) I've run a handful of subjects through mri_convert and the recon
>stream
> and each subject has a slight abnormality in the ventral temporal
>regions.
> It's subtle but apparent in each acquisition (image attached and the
> abnormality is apparent at the red cross). We believed it to be an
>alignment
> issue due to the oblique slices. Is there any way to fix this
>abnormality?
>
> 2) Are there any different preprocessing steps that should be added to
> mri_convert or the recon stream?
>
> Thanks much in advance!
> Kate
>
>
> Katherine Reiter, M.S.
>
> Clinical Psychology Doctoral Student
>
> Marquette University
>
> Phone: (414) 288-3807Email: katherine.rei...@marquette.edu
>
>
>

The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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[Freesurfer] Open Research Assistant position at the VA

2016-04-13 Thread Leslie Nordstrom

Hi FreeSurfers,

There is a research assistant position opening at the VA Boston Healthcare
System in neuroimaging and aging (job announcement is attached).
This would be a great position for someone who is interested in both the
technical aspects of MRI data processing/analysis as well as in
neuropsychology and aging research.

Interested applicants should send a resume and contact information for two
references via email to Leslie Nordstrom: lesli...@bu.edu with RESEARCH
ASSISTANT as the subject line.

Please forward this message to anyone you think might be interested in the
position!


JOB_ANNOUNCEMENT_RESEARCH_ASSISTANT-2016_Aging.doc
Description: MS-Word document
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[Freesurfer] Freesurfer v6 beta

2016-04-13 Thread Francis Tyson Thomas

Hi,

I was wondering when would the new Freesurfer v6 beta be available? Also I
have been using the old beta for my hippocampal segmentation and I wanted
to know if this new beta will affect the results of that?

Thanks,
Tyson
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Re: [Freesurfer] .license and tksurfer

2016-04-13 Thread Z K

Do you have a .license file in your /Applications/freesurfer directory?

If so try making a copy of it and calling it license.txt and try again. 
If that still doesnt work please email me your .license file TO MY 
PERSONAL EMAIL ADDRESS, NOT THE FREESURFER LIST. Thanks.

-Zeke

On 04/13/2016 01:38 PM, std...@virgilio.it wrote:
> Hi list,
>
>
> please see the error reported below. It occurs when I invoke tksurfer.
>
> Of note, I have completed without problem fs-fast analysis without error.
>
> The .license file is well placed and written.
>
> Thanks
>
>
> Stefano
>
>
> tksurfer fsaverage rh inflated -aparc -overlay
> subj/rest/fc.ROI.surf.rh/ROI/sig.nii.gz -fminmax 1.3 3
>
> thresholds min=1.3 max=3 slope=0.588235 mid=2.15
>
> subject is fsaverage
>
> hemiis rh
>
> surface is inflated
>
> surfer: current subjects dir:
> /Applications/freesurfer/subjects/subject_prova
>
> surfer: not in "scripts" dir ==> using cwd for session root
>
> surfer: session root data dir ($session) set to:
>
> surfer: /Applications/freesurfer/subjects/fMRI/con_run1
>
> checking for nofix files in 'inflated'
>
> Reading image info
> (/Applications/freesurfer/subjects/subject_prova/fsaverage)
>
> Reading
> /Applications/freesurfer/subjects/subject_prova/fsaverage/mri/orig.mgz
>
> surfer: Reading header info from
> /Applications/freesurfer/subjects/subject_prova/fsaverage/mri/orig.mgz
>
> --
>
> ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
>
>If you are outside the NMR-Martinos Center,
>
>go to http://surfer.nmr.mgh.harvard.edu to
>
>get a valid license file (it's free).
>
>If you are inside the NMR-Martinos Center,
>
>make sure to source the standard environment.
>
>
>
> ___
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[Freesurfer] .license and tksurfer

2016-04-13 Thread stdp82

Hi list,
please see the error reported below. It occurs when I invoke tksurfer.Of note, 
I have completed without problem fs-fast analysis without error.The .license 
file is well placed and written.Thanks
Stefano
tksurfer fsaverage rh inflated -aparc -overlay 
subj/rest/fc.ROI.surf.rh/ROI/sig.nii.gz -fminmax 1.3 3
thresholds min=1.3 max=3 slope=0.588235 mid=2.15
subject is fsaverage
hemiis rh
surface is inflated
surfer: current subjects dir: /Applications/freesurfer/subjects/subject_prova
surfer: not in "scripts" dir ==> using cwd for session root
surfer: session root data dir ($session) set to:
surfer: /Applications/freesurfer/subjects/fMRI/con_run1
checking for nofix files in 'inflated'
Reading image info (/Applications/freesurfer/subjects/subject_prova/fsaverage)
Reading /Applications/freesurfer/subjects/subject_prova/fsaverage/mri/orig.mgz
surfer: Reading header info from 
/Applications/freesurfer/subjects/subject_prova/fsaverage/mri/orig.mgz
--
ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.
  If you are outside the NMR-Martinos Center,
  go to http://surfer.nmr.mgh.harvard.edu to 
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.___
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Re: [Freesurfer] Oblique Slice Acquisition

2016-04-13 Thread Bruce Fischl


Hi Kate

I don't think that will matter. Try running it through from the original 
dicoms and see if things seem accurate. That isn't actually an artifact, 
it just looks strange because of the slight angle of the view. My guess is 
we will handle this fine


cheers
Bruce

On Wed, 13 Apr 
2016, Katherine Reiter wrote:



Hello freesurfer experts,
I am working with a dataset that was acquired with oblique slices aligned to
each participant's ac-pc line.

1) I've run a handful of subjects through mri_convert and the recon stream
and each subject has a slight abnormality in the ventral temporal regions.
It's subtle but apparent in each acquisition (image attached and the
abnormality is apparent at the red cross). We believed it to be an alignment
issue due to the oblique slices. Is there any way to fix this abnormality?

2) Are there any different preprocessing steps that should be added to
mri_convert or the recon stream?

Thanks much in advance!
Kate


Katherine Reiter, M.S.

Clinical Psychology Doctoral Student

Marquette University

Phone: (414) 288-3807Email: katherine.rei...@marquette.edu



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Re: [Freesurfer] mri_vol2surf after recon-all

2016-04-13 Thread Trisanna Sprung-Much

Hi Doug

So I tried running mni152reg and had the following error:

mni152reg --s icbm-102_test


setenv SUBJECTS_DIR /data-01/trisanna/freesurfer
cd /home/trisanna
/usr/local/freesurfer-5.3//bin/mni152reg --s icbm-102_test


fslregister --mov
/usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --s
icbm-102_test --reg
/data-01/trisanna/freesurfer/icbm-102_test/mri/transforms/reg.mni152.2mm.dat
--dof 12
mkdir: cannot create directory
‘/usr/share/fsl/5.0/data/standard/tmp.fslregister.11061’: Permission denied

I spoke with our IT guy and he says that of course I cannot be writing to
fsl/5.0/data. I then did a web search and found that someone else was
having this problem

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41276.html

How might I fix this? Let me know if I should send the log file that was
created.

best

Trisanna


--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Apr 8, 2016 at 1:33 PM, Douglas N Greve 
wrote:

> not sure, mni152reg uses $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz
>
> You can always just run the following command directly
>
> fslregister --mov icbm.nii.gz --s $subject --reg
> $SUBJECTS_DIR/subject/transforms/icbm.reg.dat --dof 12
>   --lta $SUBJECTS_DIR/subject/transforms/icbm.reg.lta
>
> This will use a linear (12 dof) registration which might not be
> particularly accurate
>
>
> On 04/08/2016 01:27 PM, Trisanna Sprung-Much wrote:
> > thanks, Doug. I'll get started on running all brains using recon-all.
> >
> > The MNI has several ICBM templates now:
> >
> > ICBM152 linear
> > ICBM152 nonlinear symmetric VI
> > ICBM152 nonlinear 2009
> >
> > Do you know which one mni152reg is using?
> >
> > Trisanna
> >
> > --
> > Ph.D. Candidate
> > McGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> > On Fri, Apr 8, 2016 at 12:47 PM, Douglas N Greve
> > > wrote:
> >
> >
> >
> > On 04/07/2016 03:50 PM, Trisanna Sprung-Much wrote:
> > > thanks, Doug. I am still extremely confused, however. *Am I meant
> to
> > > run recon-all first? *I was told in a previous email that I
> > should do
> > > this first, however, I thought that Freesurfer takes the volumes
> and
> > > does a linear registration to MNI305 template, which would not work
> > > for my scans that are linearly registered to ICBM152 nonlinear 2006
> > > template...
> > run recon-all first, otherwise you won't have surfaces. recon-all
> > computes the transform matrix to the mni305 but keeps all the data in
> > the native anatomical space. I think the ICBM152 is the same as the
> > MNI152. Is that right? If so, you can use mni152reg to compute the
> > registration to 152 space. If not, then we'll have to workout
> > something
> > else.
> > >
> > > When you have a moment, could you please outline in a step by step
> > > manner the steps I should run to take my labels.mnc and my volumes
> > > such that I can generate surfaces for those 50 volumes, overlay the
> > > labels (for which I thought I was using mri_vol2surf) and then edit
> > > those labels to make them more accurate?
> > so you want to transfer the labels from labels.mnc to the surfaces of
> > your individual 50 subjects? Start by running recon-all on the 50.
> > > *The idea is that I want to generate some sulcal probability maps
> > > using surface-based registration, as I can already generate
> > > probability maps using volumetric registration quite easily.*
> > >
> > > many thanks
> > >
> > > Trisanna
> > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > > Ph.D. Candidate
> > > McGill University
> > > Integrated Program in Neuroscience
> > > Psychology
> > >
> > >
> > > On Wed, Apr 6, 2016 at 2:43 PM, Douglas Greve
> > > 
> >  > >> wrote:
> > >
> > > For the 152, you can run mni152reg --s subject, then specify
> > > $SUBJECTS_DIR/subject/mri/transform/mni152reg.dat (or .lta) for
> > > the argument to --reg. I'll need to figure out how to generate
> a
> > > .dat/.lta for the 305.
> > >
> > >
> > >
> > > On 4/6/16 12:50 PM, Trisanna Sprung-Much wrote:
> > >> Any ideas?
> > >>
> > >> Trisanna
> > >>
> > >> --
> > >> Ph.D. Candidate
> > >> McGill University
> > >> Integrated Program in Neuroscience
> > >> Psychology
> > >>
> > >>
> > >> On Tue, Apr 5, 2016 at 9:37 PM, Trisanna Sprung-Much
> > >>  > 
> > >>  >

[Freesurfer] DLPFC seed

2016-04-13 Thread Raney, Talia L.

Hi all,
I'm trying to do FC connectivity analysis using the dorsalateral prefrontal 
cortex as a seed. I checked the text file 
$FREESURFER_HOME/average/colortable_desikan_killiany.txt and it looks like 
DLPFC is not listed as a possible structure to do the FC analysis. I attempted 
to use lh-prefrontal and rh-prefrontal but selxavg3-sess fails because there's 
no volume/label in fsaverage that is associated with it. Any suggestions on 
what seeds I could use? Would I have to combine or parcellate other existing 
seeds?
Thank you!
Best,
Talia
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Re: [Freesurfer] TRACULA

2016-04-13 Thread Z K

I could be wrong, but the output in your email oscillates between 
"/Users" and "Users" (Note the preceding forward slash). Im not sure if 
thats just a copy/paste thing or directly related to your error.

-Zeke

On 04/12/2016 08:44 PM, Jasmin Alves wrote:
>
>
> So I have specified where the DTI file is. I am not sure why Tracula
> cannot open it. Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz this is
> where the the dti file is.
>
>
> On Tue, Apr 12, 2016 at 11:45 AM, Alan Francis  > wrote:
>
> Hi Jasmin -
>
> When replying please cc the FS group so that they may weigh in on
> the situation. Looking at the log, they key problem appears to be this:
>
> niiRead(): error opening file
> Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz
>
> Tracula is not able to open your DTI.nii.gz
>
> Please check this file or pathway.
>
> best,
>
> Alan
>
>
>
> On Tue, Apr 12, 2016 at 11:17 AM, Jasmin Alves  > wrote:
>
> Hi Alan,
>
> Thank you for your reply. I changed the pathway but now have
> stumbled upon a new error. I tried looking through the feeds and
> couldn't really find a relevant solution.
>
> Jasmins-MacBook-Pro:data jasminalves$ trac-all -prep -c dmrirc.txt
>
> INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER
>
> INFO: Diffusion root is /Users/jasminalves/Desktop/data/FREESURFER
>
> Actual FREESURFER_HOME /Applications/freesurfer
>
> trac-preproc -c
> /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/dmrirc.local
> -log
> /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/trac-all.log
> -cmd
> /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/trac-all.cmd
>
> #-
>
> /Applications/freesurfer/bin/trac-preproc
>
> #-
>
> #@# Image corrections Tue Apr 12 08:04:37 PDT 2016
>
> mri_convert Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz
> /Users/jasminalves/Desktop/data/FREESURFER/40/dmri/dwi_orig.nii.gz
>
> mri_convert Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz
> /Users/jasminalves/Desktop/data/FREESURFER/40/dmri/dwi_orig.nii.gz
>
> niiRead(): error opening file
> Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz
>
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>
> reading from Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz...
>
> Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version
> 14.5.0: Tue Sep  1 21:23:09 PDT 2015;
> root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
>
> trac-preproc exited with ERRORS at Tue Apr 12 08:04:37 PDT 2016
>
> Your help would be appreciated.
>
> Thank you,
>
> Jasmin
>
>
> On Tue, Apr 12, 2016 at 7:26 AM, Alan Francis
>  > wrote:
>
> Hi Jasmin -
>
> In your dmrirc file , the dcmlist refers to the dicom list.
> You have put the BVEC/BVAL files there. That is not correct.
> You need to place the actual pathway to your niftis in this
> position.
>
> set subjlist = (40 39 36)
>
> # Input diffusion DICOMs (file names relative to dcmroot)
> # If original DICOMs don't exist, these can be in other
> image format
> # but then bvecfile and bvalfile must be specified
> #
> set dcmroot = Users/jasminalves/Desktop/data/DTI
> set dcmlist = (40/DTI.nii.gz DTI.bvec DTI.bval 39/DTI.nii.gz
> DTI.bvec DTI.bval 36/DTI.nii.gz DTI.bvec DTI.bval) *<-
> Pathway to NIFTIS HERE*
>
> Hope this helps,
>
> best,
>
> Alan
>
>
> --
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|**
> *
> Alan N. Francis PhD*
> Instructor - Imaging Neuroscience
> Brain Imaging Center
> McLean Hospital
> Harvard Medical School
> 115 Mill Street, Belmont, MA 02478
> al...@bwh.harvard.edu
> 
> afran...@mclean.harvard.edu
> 
>
> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>
>
>
>
> --
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu 
>
>
>
>
> --

[Freesurfer] Summer School "Advanced Scientific Programming in Python" in Reading, UK, September 5--11, 2016

2016-04-13 Thread Etienne B. Roesch

*Advanced Scientific Programming in Python*

a Summer School by the G-Node, and the Centre for Integrative Neuroscience
and Neurodynamics, School of Psychology and Clinical Language Sciences,
University of Reading, UK

Scientists spend more and more time writing, maintaining, and debugging
software. While techniques for doing this efficiently have evolved, only
few scientists have been trained to use them. As a result, instead of doing
their research, they spend far too much time writing deficient code and
reinventing the wheel. In this course we will present a selection of
advanced programming techniques and best practices which are standard in
the industry, but especially tailored to the needs of a programming
scientist. Lectures are devised to be interactive and to give the students
enough time to acquire direct hands-on experience with the materials.
Students will work in pairs throughout the school and will team up to
practice the newly learned skills in a real programming project — an
entertaining computer game.

We use the Python programming language for the entire course. Python works
as a simple programming language for beginners, but more importantly, it
also works great in scientific simulations and data analysis. We show how
clean language design, ease of extensibility, and the great wealth of open
source libraries for scientific computing and data visualization are
driving Python to become a standard tool for the programming scientist.

This school is targeted at Master or PhD students and Post-docs from all
areas of science. Competence in Python or in another language such as Java,
C/C++, MATLAB, or Mathematica is absolutely required. Basic knowledge of
Python and of a version control system such as git, subversion, mercurial,
or bazaar is assumed. Participants without any prior experience with Python
and/or git should work through the proposed introductory material before
the course.

We are striving hard to get a pool of students which is international and
gender-balanced.

You can apply online: https://python.g-node.org



*Application deadline: 23:59 UTC, May 15, 2016. Be sure to read the FAQ
before applying. *

Participation is for free, i.e. no fee is charged! Participants however
should take care of travel, living, and accommodation expenses by
themselves. Travel grants may be available.


*Date & Location *
September 5—11, 2016. Reading, UK

*Program *
- Best Programming Practices
• Best practices for scientific programming
• Version control with git and how to contribute to open source projects
with GitHub
• Best practices in data visualization

- Software Carpentry
• Test-driven development
• Debugging with a debugger
• Profiling code

- Scientific Tools for Python
• Advanced NumPy

- Advanced Python
• Decorators
• Context managers
• Generators

- The Quest for Speed
• Writing parallel applications
• Interfacing to C with Cython
• Memory-bound problems and memory profiling
• Data containers: storage and fast access to large data

- Practical Software Development
• Group project

*Preliminary Faculty *
• Francesc Alted, freelance consultant, author of PyTables, Spain
• Pietro Berkes, Enthought Inc., Cambridge, UK
• Zbigniew Jędrzejewski-Szmek, Krasnow Institute, George Mason University,
Fairfax, VA, USA
• Eilif Muller, Blue Brain Project, École Polytechnique Fédérale de
Lausanne, Switzerland
• Juan Nunez-Iglesias, Victorian Life Sciences Computation Initiative,
University of Melbourne, Australia
• Rike-Benjamin Schuppner, Institute for Theoretical Biology,
Humboldt-Universität zu Berlin, Germany
• Bartosz Teleńczuk, European Institute for Theoretical Neuroscience, CNRS,
Paris, France
• Stéfan van der Walt, Berkeley Institute for Data Science, UC Berkeley,
CA, USA
• Nelle Varoquaux, Centre for Computational Biology Mines ParisTech,
Institut Curie, U900 INSERM, Paris, France
• Tiziano Zito, freelance consultant, Germany

*Organizers *
For the German Neuroinformatics Node of the INCF (G-Node) Germany:
• Tiziano Zito, freelance consultant, Germany
• Zbigniew Jędrzejewski-Szmek, Krasnow Institute, George Mason University,
Fairfax, USA
• Jakob Jordan, Institute of Neuroscience and Medicine (INM-6),
Forschungszentrum Jülich GmbH, Germany

For the Centre for Integrative Neuroscience and Neurodynamics, School of
Psychology and Clinical Language Sciences, University of Reading UK:
• Etienne Roesch, Centre for Integrative Neuroscience and Neurodynamics,
University of Reading, UK

*Website*: https://python.g-node.org
*Contact*: python-i...@g-node.org


Kind regards,

Etienne

-
Dr. Etienne B. Roesch
Lecturer in Cognitive Science
University of Reading
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[Freesurfer] MatrixMultiply: m2 is null error, trying to convert MNI152 ROI to FreeSurfer label

2016-04-13 Thread DeCross, Stephanie N.

Hi,

I’m trying to take an ROI in MNI152 volume space and make it into a cortical 
surface label, for visualization purposes.

With my input being the lh thresholded, binarized MNI152 nii.gz label (when I 
visualize it, it looks as it should in fslview), I ran:

mri_vol2vol -- mov   -- targ 
$SUBJECTS_DIR/fsaverage/mri/orig.mgz  -- o   -- regheader  
-- talres 2  -- interp nearest

mri_cor2label -- c   -- id 1  -- l  
./

My commands above seem to have run fine, but when I open the lh in tksurfer and 
try to load the new lh label file, the dialogue runs for a little but then 
errors out:

12304 unassigned vertices in label - building spatial LUT…
assigning vertex numbers to label...
MatrixMultiply: m2 is null!

And then tksurfer closes. I’m not sure what’s going wrong - does anyone have 
any pointers or troubleshooting methods I can try?

Thanks,
Stephanie

Stephanie N. DeCross
Clinical Research Coordinator
Psychiatric Neuroimaging Research Program
Martinos Center for Biomedical Imaging
Massachusetts General Hospital
149 13th Street, Rm 2620A
Charlestown, MA 02129
Phone: (617) 724-3283
Fax: (617) 726-4078


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Re: [Freesurfer] mri_surfcluster issues

2016-04-13 Thread Antonin Skoch

Dear Doug,

thank you very much for the support.

I am quite confused by this info about correcting of area of fsaverage 
clusters. Could you please clarify to me the following:

How exactly the values of lh.area, lh.white.avg.area.mgh of fsaverage were 
computed?

How the cluster area inside mri_surfcluster (and also mri_glmfit and mri_mcsim) 
is computed?

How the correction for average subject is applied?

I assumed that area belonging to particular vertex is computed by summing areas 
of faces originating in particular vertex divided by 3.
The face areas are computed from vertex coordinates by the method (based on 
cross-product of vectors)

http://stackoverflow.com/questions/26312570/calculate-surface-area-of-a-3d-mesh

This is how the vertex area from surface file is computed inside PALM. Is the 
same method used in freeSurfer? I checked the values of lh.white vertex area 
computed in PALM and they do NOT correspond neither to lh.area, nor 
lh.white.area.mgh values.
I am listing areas of 3 representative vertices of fsaverage white surface got 
from lh.white.avg.area, lh.area and computed from lh.white in PALM:

vtx 50: lh.white.avg.area 0.4952, lh.area 0.589, PALM 0.5967
vtx 110: lh.white.avg.area 0.5533, lh.area 0.5198, PALM 0.5421
vtx 1000: lh.white.avg.area 0.6193, lh.area 0.3349, PALM 0.4305

Any clues why there is a difference?

In cluster summary file, there are flags FixVertexAreaFlag 1 and 
FixSurfClusterArea 1. What is the significance of these flags? I tried to set 
--no-fix-vertex-area. The FixVertexAreaFlag got value 0, but the vertex areas 
produced by mri_surfcluster were the same.
Is it possible to turn off also FixSurfClusterArea?

I also found flags FixVertexAreaFlag and FixGroupSubjectArea in .csd files. Are 
there similar corrections applied to cluster size values in .csd files?

Thank you in advance for help. 

Regards,

Antonin Skoch

> Dear FreeSurfer experts,
>
> I am using mri_surfcluster to compare results from PALM and FreeSurfer 
> cluster extent inference.
>
> I came across several issues in mri_surfcluster I cannot cope with.
>
> 1.
> I observed that --mask option in mri_surfcluster does not prevent 
> cluster to growing outside the mask.
>
> When I run
>
> mri_surfcluster --in lh.thickness.fsaverage_masked.mgh --sum 
> summary.txt --subject fsaverage --surf white --hemi lh --thmin 0 --ocn 
> cluster_summary.mgz --mask ./mask.mgh
>
> the cluster is growing outside mask and covers all surface including 
> non-cortical (masked) regions.
>
> Is this intended behavior? This behavior (allowing clusters leak 
> outside mask) seems strange to me since it could possibly influence 
> results of cluster-extent inference in case of mask-constrained analysis.
This is happening because you are setting the threshold to 0.
>
> 2.
> How behaves mri_glmfit-sim in permutation-based building 
> cluster-extent null distribution with mask? Is in this case also 
> allowed to clusters to leak outside mask?
No
>
> 3.
> Another issue is concerning reported cluster area. I tested 
> mri_surfcluster on data where overlay values 
> (lh.thickness.fsaverage.mgh) were set to 0 outside cortex mask (they 
> were non-zero also in some portion of non-cortical vertices). When I 
> set thmin to non-zero value in mri_surfcluster
>
> mri_surfcluster --in lh.thickness.fsaverage_masked.mgh --sum 
> summary.txt --subject fsaverage --surf white --hemi lh --thmin 0.1 
> --ocn cluster_summary.mgz --mask ./mask.mgh
>
> I get cluster comprising (almost) all cortex, not leaking to 
> non-cortical areas. But what is strange, the reported cluster size is 
> far larger than area of the whole cortical surface.
>
> number of voxels in search space = 149953
> Done loading source values (nvtxs = 163842)
> overall max = 5 at vertex 817
> overall min = 0 at vertex 8
> surface nvertices 163842
> surface area 65417.097656
> surface area 65416.648438
> NOT Adjusting threshold for 1-tailed test
> Searching for Clusters ...
> thmin=0.000100 (0.000100), thmax=-1.00 (-1), thsignid=0, 
> minarea=0.00
> Found 2 clusters
> Max cluster size 76431.562500
> Saving cluster numbers to pok.mgz
>
>
> Here is output of mri_surfcluster:
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZ NVtxs
>15.000 817  76431.56-25.84.6  -37.5  149874
>22.670  144205  0.53-15.8  -40.4   -3.8 1
>
> How it is possible?
The surface area of 65416.648438 has not been corrected for the fact 
that fsaverage is an average subject. The area in the summary table has 
been corrected.
>
> 4.
> Does the fsaverage/surf/lh.area correspond to area of particular 
> vertices on fsaverage/surf/lh.white? I expect yes.
The lh.area file does correspond. However, the area measures on the raw 
fsaverage surface are not accurate because the average surface has much 
less surface area due to averaging out the individual folding patterns.
>
> 5.
> How it is possible to calculate area of specified vertex of surface? I

Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

2016-04-13 Thread Clara Kühn

Thank you!

- Ursprüngliche Mail -
Von: "Douglas Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 13. April 2016 16:46:19
Betreff: Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

In most neuroimaging, people use p<.01 (sig threshold > 2). It is more 
important to have a more stringent threshold when using gaussian random 
fields because the assumptions built into it. Since we use simulations 
directly, we don't have problems with those assumptions and so I think 
you can go down to p<.05 (sig>1.3). Other than that, there are not good 
guidelines.

On 4/13/16 8:36 AM, Clara Kühn wrote:
> Hi Doug,
>
> thanks for your reply. It made things a lot clearer. I totally understand 
> that you're probably receiving more than one cry for help per day.
>
> What would you say are the conventions for picking a threshold for analyses 
> on structural data?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 13. April 2016 00:15:41
> Betreff: Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC
>
> sorry, I could have sworn that I answered this one
>
> On 04/12/2016 08:57 AM, Clara Kühn wrote:
>> Dear FreeSurfer experts,
>>
>> for the analysis in QDEC I created my own Monte Carlo correction.
>> My questions relate to the threshold option.
>>
>> 1. Would I use neg if I have mostly blue clusters in the QDEC display and 
>> pos if I have mostly red clusters?
> No, you would use neg when you have an apriori assumption that your
> effect is going to be negative. Once you look at the results, it is no
> long apriori
>> 2. When do I use abs?
> If you do not have an apriori assumption about the sign of the effect
>> 3. I compared the neg option at different thresholds (1.3, 2.0 and 2.3) and 
>> I get different clusters:
>> 1.3 (=.05)
>> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow  
>>   CWPHi   NVtxs   Annot
>>  1   -2.669   76591   1148.00 -6.7   14.5   62.7  0.00880  
>> 0.00760  0.01000  1600  superiorfrontal
>>  2   -2.443   91912   2128.78-10.3   55.3  -23.5  0.00010  
>> 0.0  0.00020  2971  medialorbitofrontal
>>
>> 2.0 (=.01)
>> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow  
>>   CWPHi   NVtxs   Annot
>>  1   -3.289   92754420.03-36.5   57.0  -21.0  0.02140  
>> 0.01960  0.02330   571  parsorbitalis
>>  2   -2.669   76591428.11 -6.7   14.5   62.7  0.01940  
>> 0.01760  0.02120   604  superiorfrontal
>>
>> 2.3 (=.005)
>> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow  
>>   CWPHi   NVtxs   Annot
>>  1   -3.289   92754314.80-36.5   57.0  -21.0  0.01900  
>> 0.01730  0.02080   410  parsorbitalis
>>
>> Technically, if parsorbitalis is significant at .01 and .005, shouldn't it 
>> also be significant at .05? I've compared the clusters in freeview and the 
>> superiorfrontal is the same cluster in both 1.3 and 2.0. The parsorbitalis 
>> and the medialorbitofrontal clusters are completely different, not even 
>> closely overlapping.
> You are confusing the two types of thresholds. The voxel-wise threshold
> that you are changing defines what is and is not a cluster. As you
> change it clusters will change size. As you make it more liberal, you
> make it more likely that you see a cluster of a certain size by chance
> (ie, the p-value for the cluster gets worse). So as you make the
> threshold more liberal, there are two competing effects: (1) the cluster
> gets bigger, and (2) the p-value of a cluster of a given fixed size gets
> worse. If the cluster size does not increase enough to overcome the
> second effect, then the cluster p-value will get worse. It is just very
> complicated.
>
>> Do you have any idea why that is and what it does differently?
>> Thank you!
>> Cheers, Clara
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>

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Re: [Freesurfer] correcting mri_glmfit results

2016-04-13 Thread Douglas Greve

Looks like you are analyzing a table of data (ie, ROI analysis). In this 
case you cannot use clusterwise correction because you cannot form 
clusters of voxels when you don't have a voxel-wise analysis! You can do 
a bonferroni or FDR correction. You can get an FDR program from here 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_fdr
doug

On 4/13/16 8:40 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I'm trying to run a mri_glmfit on my first time point (out of 3). I ran the 
> glm with this:
> mri_glmfit --table $SUBJECTS_DIR/aparcs_stats_sc1.txt --fsgd 
> $SUBJECTS_DIRfsgd_sc1.txt --C $SUBJECTS_DIR/group.mtx --surf 87kids_template 
> lh --cortex --glmdir $SUBJECTS_DIR/glm/lh.thick_group.glmdir
>
> So far so good :)
>
> Now when I try to apply the Monte Carlo correction with this:
> mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/glm/lh.thick_group.glmdir 
> --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 neg --cwp 0.05 
> --2spaces
>
> I get the error "fwhm: Undefined variable."
>
> So I tried to run the glmfit with the --y flag and use the 
> lh.thickness_sm10.mgh file but I created that when registering and smoothing 
> ALL my time points to the template, so I get this error: "ERROR: dimension 
> mismatch between y and X. y has 224 inputs, X has 72 rows."
>
> I have looked at mri_glmfit-sim --help but there seems to be no flag for fwhm 
> only an overwriting one.
>
> Should I register and smooth the data again for the separate time points or 
> is there another way to deal with that?
> What could I do to correct my glm data?
>
> Cheers, Clara

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Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

2016-04-13 Thread Douglas Greve

In most neuroimaging, people use p<.01 (sig threshold > 2). It is more 
important to have a more stringent threshold when using gaussian random 
fields because the assumptions built into it. Since we use simulations 
directly, we don't have problems with those assumptions and so I think 
you can go down to p<.05 (sig>1.3). Other than that, there are not good 
guidelines.

On 4/13/16 8:36 AM, Clara Kühn wrote:
> Hi Doug,
>
> thanks for your reply. It made things a lot clearer. I totally understand 
> that you're probably receiving more than one cry for help per day.
>
> What would you say are the conventions for picking a threshold for analyses 
> on structural data?
>
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve" 
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mittwoch, 13. April 2016 00:15:41
> Betreff: Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC
>
> sorry, I could have sworn that I answered this one
>
> On 04/12/2016 08:57 AM, Clara Kühn wrote:
>> Dear FreeSurfer experts,
>>
>> for the analysis in QDEC I created my own Monte Carlo correction.
>> My questions relate to the threshold option.
>>
>> 1. Would I use neg if I have mostly blue clusters in the QDEC display and 
>> pos if I have mostly red clusters?
> No, you would use neg when you have an apriori assumption that your
> effect is going to be negative. Once you look at the results, it is no
> long apriori
>> 2. When do I use abs?
> If you do not have an apriori assumption about the sign of the effect
>> 3. I compared the neg option at different thresholds (1.3, 2.0 and 2.3) and 
>> I get different clusters:
>> 1.3 (=.05)
>> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow  
>>   CWPHi   NVtxs   Annot
>>  1   -2.669   76591   1148.00 -6.7   14.5   62.7  0.00880  
>> 0.00760  0.01000  1600  superiorfrontal
>>  2   -2.443   91912   2128.78-10.3   55.3  -23.5  0.00010  
>> 0.0  0.00020  2971  medialorbitofrontal
>>
>> 2.0 (=.01)
>> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow  
>>   CWPHi   NVtxs   Annot
>>  1   -3.289   92754420.03-36.5   57.0  -21.0  0.02140  
>> 0.01960  0.02330   571  parsorbitalis
>>  2   -2.669   76591428.11 -6.7   14.5   62.7  0.01940  
>> 0.01760  0.02120   604  superiorfrontal
>>
>> 2.3 (=.005)
>> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow  
>>   CWPHi   NVtxs   Annot
>>  1   -3.289   92754314.80-36.5   57.0  -21.0  0.01900  
>> 0.01730  0.02080   410  parsorbitalis
>>
>> Technically, if parsorbitalis is significant at .01 and .005, shouldn't it 
>> also be significant at .05? I've compared the clusters in freeview and the 
>> superiorfrontal is the same cluster in both 1.3 and 2.0. The parsorbitalis 
>> and the medialorbitofrontal clusters are completely different, not even 
>> closely overlapping.
> You are confusing the two types of thresholds. The voxel-wise threshold
> that you are changing defines what is and is not a cluster. As you
> change it clusters will change size. As you make it more liberal, you
> make it more likely that you see a cluster of a certain size by chance
> (ie, the p-value for the cluster gets worse). So as you make the
> threshold more liberal, there are two competing effects: (1) the cluster
> gets bigger, and (2) the p-value of a cluster of a given fixed size gets
> worse. If the cluster size does not increase enough to overcome the
> second effect, then the cluster p-value will get worse. It is just very
> complicated.
>
>> Do you have any idea why that is and what it does differently?
>> Thank you!
>> Cheers, Clara
>> ___
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>>
>>

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Re: [Freesurfer] glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)

2016-04-13 Thread Douglas Greve

Try it without the --no-sim. The --no-sim was from before I stored the 
cached data and you either had to run a simulation or not.


On 4/12/16 9:10 PM, Pedro Rosa wrote:

Dear list,
I want to limit my vertex-wise group analysis to a smaller spatial 
region, then I ran my own Monte-Carlo simulation on fsaverage for the 
superior temporal gyrus:


mri_mcsim --o lh/superiortemporal --base mc-z --surface /fsaverage lh 
--nreps 1 --label superiortemporal



After 36 hours, it finished and I pasted the resulting into 
$FREESURFER_HOME/average/mult-comp-cor/fsaverage, and ran glmfit:


mri_glmfit --glmdir glmdir --y lh.thickness.5.mgh --fsgd table.fsgd 
--C contrast.mtx --surface fsaverage lh --label 
/$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label


It seems it ran only on the label, as expected.

However I am not able touse this pre-cached simulation in mri_glmfit-sim.

I tried: mri_glmfit-sim --glmdir glmdir --sim-sign abs --cache-dir 
$FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/superiortemporal 
--no-sim mc-z.abs.th13 --cache-label 
/$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label



...but I get an error although the csd files are in 
/average/mult-comp-cor/fsaverage... path : ERROR: cannot find any csd 
files


I tried several combinations of the text specified after --no-sim, but 
all I got is the error above. I though I should refer to my own 
simulation using --cache-dir, but it requires the --no-sim flag.


Can anyone help me?

Best,

Pedro Rosa.





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Re: [Freesurfer] correcting mri_glmfit results

2016-04-13 Thread Martin Reuter

Hi Clara,
You need to register and smooth again for only the first time point. 
You could also open the full stack in Matlab, select the entries of your first time point and write it out again.
Best Martin
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Re: [Freesurfer] PET voxelwise

2016-04-13 Thread Elijah Mak

Hi Doug,

One more question about feeding the -reg to mri_vol2surf, please.

I am specifying the registration .lta because I have made edits to it,

mri_vol2surf --src FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out
FS6_24551_MPRAGE_Neuro.nii/surf/lh.PETSurfce.mgh --projfrac 0.5 --hemi lh
--reg FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz.lta --trgsubject
fsaverage

I get the following error:

srcvol = FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz

srcreg = FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz.lta

srcregold = 0

srcwarp unspecified

surf = white

hemi = lh

trgsubject = fsaverage

surfreg = sphere.reg

ProjFrac = 0.5

thickness = thickness

reshape = 0

interp = nearest

float2int = round

GetProjMax = 0

INFO: float2int code = 0

Done loading volume

Input reg is LTA



type  = 0 # LINEAR_VOX_TO_VOX

nxforms   = 1

mean  = 0. 0. 0.

sigma = 1.

1 4 4

9.996573328971863e-01 -2.963314531370997e-03 2.600867860019207e-02
-2.005096435546875e+00

1.517883041479706e-18 9.935718178749084e-01 1.132032126188278e-01
-2.398274230957031e+01

-2.617694810032845e-02 -1.131644248962402e-01 9.932314157485962e-01
1.568508148193359e+01

0.000e+00 0.000e+00 0.000e+00
1.000e+00

src volume info

valid = 1  # volume info valid

filename =
/Users/MacPro/Documents/NIMROD_DTI/FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz

volume = 256 256 256

voxelsize = 1.000e+00 1.000e+00
1.000e+00

xras   = -1.000e+00 -2.328306436538696e-10 0.000e+00

yras   = -1.862645149230957e-09 -2.991509973071516e-08
-1.000e+00

zras   = 0.000e+00 1.000e+00 1.091393642127514e-10

cras   = 1.471549987792969e+00 -1.038517761230469e+01 1.970146179199219e+01

dst volume info

valid = 1  # volume info valid

filename =
/Users/MacPro/Documents/NIMROD_DTI/FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz

volume = 256 256 256

voxelsize = 1.000e+00 1.000e+00
1.000e+00

xras   = -1.000e+00 -2.328306436538696e-10 0.000e+00

yras   = -1.862645149230957e-09 -2.991509973071516e-08
-1.000e+00

zras   = 0.000e+00 1.000e+00 1.091393642127514e-10

cras   = 1.471549987792969e+00 -1.038517761230469e+01 1.970146179199219e+01

fscale 0.15

ERROR: source volume is neither source nor target of the registration

This error does not appear when I use --regheader though?

Best Wishes,

Elijah
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[Freesurfer] correcting mri_glmfit results

2016-04-13 Thread Clara Kühn


Dear FreeSurfer experts,

I'm trying to run a mri_glmfit on my first time point (out of 3). I ran the glm 
with this:
mri_glmfit --table $SUBJECTS_DIR/aparcs_stats_sc1.txt --fsgd 
$SUBJECTS_DIRfsgd_sc1.txt --C $SUBJECTS_DIR/group.mtx --surf 87kids_template lh 
--cortex --glmdir $SUBJECTS_DIR/glm/lh.thick_group.glmdir

So far so good :)

Now when I try to apply the Monte Carlo correction with this:
mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/glm/lh.thick_group.glmdir 
--cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 neg --cwp 0.05 
--2spaces

I get the error "fwhm: Undefined variable."

So I tried to run the glmfit with the --y flag and use the 
lh.thickness_sm10.mgh file but I created that when registering and smoothing 
ALL my time points to the template, so I get this error: "ERROR: dimension 
mismatch between y and X. y has 224 inputs, X has 72 rows."

I have looked at mri_glmfit-sim --help but there seems to be no flag for fwhm 
only an overwriting one.

Should I register and smooth the data again for the separate time points or is 
there another way to deal with that?
What could I do to correct my glm data?

Cheers, Clara
-- 
Clara Kühn, Phd Student
 
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany

Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.mpg.de

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Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

2016-04-13 Thread Clara Kühn

Hi Doug, 

thanks for your reply. It made things a lot clearer. I totally understand that 
you're probably receiving more than one cry for help per day.

What would you say are the conventions for picking a threshold for analyses on 
structural data? 

Cheers, Clara

- Ursprüngliche Mail -
Von: "Douglas N Greve" 
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 13. April 2016 00:15:41
Betreff: Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

sorry, I could have sworn that I answered this one

On 04/12/2016 08:57 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> for the analysis in QDEC I created my own Monte Carlo correction.
> My questions relate to the threshold option.
>
> 1. Would I use neg if I have mostly blue clusters in the QDEC display and pos 
> if I have mostly red clusters?
No, you would use neg when you have an apriori assumption that your 
effect is going to be negative. Once you look at the results, it is no 
long apriori
>
> 2. When do I use abs?
If you do not have an apriori assumption about the sign of the effect
>
> 3. I compared the neg option at different thresholds (1.3, 2.0 and 2.3) and I 
> get different clusters:
> 1.3 (=.05)
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow   
>  CWPHi   NVtxs   Annot
> 1   -2.669   76591   1148.00 -6.7   14.5   62.7  0.00880  0.00760 
>  0.01000  1600  superiorfrontal
> 2   -2.443   91912   2128.78-10.3   55.3  -23.5  0.00010  0.0 
>  0.00020  2971  medialorbitofrontal
>
> 2.0 (=.01)
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow   
>  CWPHi   NVtxs   Annot
> 1   -3.289   92754420.03-36.5   57.0  -21.0  0.02140  0.01960 
>  0.02330   571  parsorbitalis
> 2   -2.669   76591428.11 -6.7   14.5   62.7  0.01940  0.01760 
>  0.02120   604  superiorfrontal
>
> 2.3 (=.005)
> # ClusterNo  Max   VtxMax   Size(mm^2)  MNIX   MNIY   MNIZCWPCWPLow   
>  CWPHi   NVtxs   Annot
> 1   -3.289   92754314.80-36.5   57.0  -21.0  0.01900  0.01730 
>  0.02080   410  parsorbitalis
>
> Technically, if parsorbitalis is significant at .01 and .005, shouldn't it 
> also be significant at .05? I've compared the clusters in freeview and the 
> superiorfrontal is the same cluster in both 1.3 and 2.0. The parsorbitalis 
> and the medialorbitofrontal clusters are completely different, not even 
> closely overlapping.
You are confusing the two types of thresholds. The voxel-wise threshold 
that you are changing defines what is and is not a cluster. As you 
change it clusters will change size. As you make it more liberal, you 
make it more likely that you see a cluster of a certain size by chance 
(ie, the p-value for the cluster gets worse). So as you make the 
threshold more liberal, there are two competing effects: (1) the cluster 
gets bigger, and (2) the p-value of a cluster of a given fixed size gets 
worse. If the cluster size does not increase enough to overcome the 
second effect, then the cluster p-value will get worse. It is just very 
complicated.

>
> Do you have any idea why that is and what it does differently?
> Thank you!
> Cheers, Clara
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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Re: [Freesurfer] missing baseline in longitudinal analysis

2016-04-13 Thread Mihaela Stefan

Hi Martin!
Sorry to bug you but I have one more question. How do I create the Qdec
table without the baseline for that subject? Do I leave the baseline time
point out or I still enter it in the table?

For example
fsid   fsid-base years
Study1_Subj1_MRI0.  Study1_Subj1.   0
Study1_Subj1_MRI1.   Study1_Subj1.   1.25
Study1_Subj1_MRI2.   Study1_Subj1.   2.25

OR

Study1_Subj1_MRI1.  Study1_Subj1.1.25
Study1_Subj1_MRI2.   Study1_Subj1.  2.25

   Thanks!
Mihaela
On Apr 12, 2016 7:13 PM, "Martin Reuter" 
wrote:

> It does not compute this. Often people use time-from-baseline for their
> analysis and control for age (@ baseline).
> Best Martin
> On Apr 12, 2016 6:23 PM, Mihaela Stefan  wrote:
>
> Thanks Martin!
>
> Related to the longitudinal analysis, should we use the demeaned age at
> baseline or the LME package automatically computes this?
>
> Thanks again!
> Mihaela
> On Apr 12, 2016 5:39 PM, "Martin Reuter" 
> wrote:
>
> Hi Michael,
> the longitudinal  image processing pipeline does not care which one is
> baseline and which are follow ups. It only cares what images belong to the
> same subject.
> So, yes you can process this one with only two tone points instead of
> three.
>
> Best Martin
> On Apr 12, 2016 5:09 PM, Mihaela Stefan  wrote:
>
> Hello FreeSurfers,
>
> We are conducting a longitudinal analysis and we have a subject who is
> missing the structural at baseline (it has fMRI data though). That subject
> returned for the 1st and the 2nd follow-up. Can we process the longitudinal
> pipeline the usual way and account for the missing baseline in the LME
> analysis?
>
> The other option would be to treat the 1st follow-up as baseline but we
> would like to be consistent with the fMRI analyses and keep the baseline
> time point.
>
> Thanks!
> Mihaela
>
>
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[Freesurfer] Repeated measures of one group analysis question

2016-04-13 Thread Martina Papmeyer

Dear FreeSurfer experts

I have a question regarding the correct data analysis method for my study
design and could unfortunately not find an example of a similar analysis on
your mailing list or documentation on the wiki.

I have repeated structural MRI data from one group (within-subjects design)
at two time points (T0 and T1). Each subject has been randomly assigned to
receive treatment or placebo either at T0 or T1 (i.e., half of them had
treatment at T0 and placebo at T1 and half of them had placebo at T0 and
treatment and T1). I am interested in the putative effects of treatment on
cortical thickness. One major challenge I face stems from the fact that the
scan interval (between T0 and T1) varies between subjects and, most
importantly, that I expect a differential impact of treatment as compared
to placebo at T0 on thickness at T1 (long-lasting increases). Thus, the
time between scans and the order of the two conditions (treatment vs
placebo) should be taken into account.

Repeated measures ANOVA seems not appropriate. I have been thinking about
conducting linear mixed effects models to analyse my data but also been
thinking about the longitudinal two-stage model you describe on the wiki. I
am unsure which method appears most appropriate and I am unsure how to
model the time between scans correctly.

Any suggestion regarding the most appropriate method and how to model the
time between scans or reference to a similar data analysis question would
be highly appreciated!

Thank you very much for your help and all best wishes, Martina
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Re: [Freesurfer] TRACULA

2016-04-13 Thread Alan Francis

Jasmin -

Check the DTI.nii.gz file using MRICRON and see if the images across the
gradients are OK. If the file is corrupt, then Tracula cannot read this.

best,

A

On Tue, Apr 12, 2016 at 8:44 PM, Jasmin Alves  wrote:

>
>
> So I have specified where the DTI file is. I am not sure why Tracula
> cannot open it. Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz this is
> where the the dti file is.
>
>
> On Tue, Apr 12, 2016 at 11:45 AM, Alan Francis 
> wrote:
>
>> Hi Jasmin -
>>
>> When replying please cc the FS group so that they may weigh in on the
>> situation. Looking at the log, they key problem appears to be this:
>>
>> niiRead(): error opening file
>> Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz
>>
>> Tracula is not able to open your DTI.nii.gz
>>
>> Please check this file or pathway.
>>
>> best,
>>
>> Alan
>>
>>
>>
>> On Tue, Apr 12, 2016 at 11:17 AM, Jasmin Alves  wrote:
>>
>>> Hi Alan,
>>>
>>> Thank you for your reply. I changed the pathway but now have stumbled
>>> upon a new error. I tried looking through the feeds and couldn't really
>>> find a relevant solution.
>>>
>>> Jasmins-MacBook-Pro:data jasminalves$ trac-all -prep -c dmrirc.txt
>>>
>>> INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER
>>>
>>> INFO: Diffusion root is /Users/jasminalves/Desktop/data/FREESURFER
>>>
>>> Actual FREESURFER_HOME /Applications/freesurfer
>>>
>>> trac-preproc -c
>>> /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/dmrirc.local -log
>>> /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/trac-all.log -cmd
>>> /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/trac-all.cmd
>>>
>>> #-
>>>
>>> /Applications/freesurfer/bin/trac-preproc
>>>
>>> #-
>>>
>>> #@# Image corrections Tue Apr 12 08:04:37 PDT 2016
>>>
>>> mri_convert Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz
>>> /Users/jasminalves/Desktop/data/FREESURFER/40/dmri/dwi_orig.nii.gz
>>>
>>> mri_convert Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz
>>> /Users/jasminalves/Desktop/data/FREESURFER/40/dmri/dwi_orig.nii.gz
>>>
>>> niiRead(): error opening file
>>> Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz
>>>
>>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>>>
>>> reading from Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz...
>>>
>>> Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0:
>>> Tue Sep  1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64
>>>
>>> trac-preproc exited with ERRORS at Tue Apr 12 08:04:37 PDT 2016
>>>
>>> Your help would be appreciated.
>>>
>>> Thank you,
>>>
>>> Jasmin
>>>
>>> On Tue, Apr 12, 2016 at 7:26 AM, Alan Francis 
>>> wrote:
>>>
 Hi Jasmin -

 In your dmrirc file , the dcmlist refers to the dicom list. You have
 put the BVEC/BVAL files there. That is not correct. You need to place the
 actual pathway to your niftis in this position.

 set subjlist = (40 39 36)

 # Input diffusion DICOMs (file names relative to dcmroot)
 # If original DICOMs don't exist, these can be in other image format
 # but then bvecfile and bvalfile must be specified
 #
 set dcmroot = Users/jasminalves/Desktop/data/DTI
 set dcmlist = (40/DTI.nii.gz DTI.bvec DTI.bval 39/DTI.nii.gz DTI.bvec
 DTI.bval 36/DTI.nii.gz DTI.bvec DTI.bval) *<- Pathway to NIFTIS HERE*

 Hope this helps,

 best,

 Alan


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 |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

 *Alan N. Francis PhD*
 Instructor - Imaging Neuroscience
 Brain Imaging Center
 McLean Hospital
 Harvard Medical School
 115 Mill Street, Belmont, MA 02478
 al...@bwh.harvard.edu
 afran...@mclean.harvard.edu


 |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

>>>
>>>
>>>
>>> --
>>> Jasmin Alves
>>> Predoctoral Student
>>> Medical Biology Graduate Program
>>> University of Southern California
>>> jal...@usc.edu
>>>
>>>
>>
>>
>> --
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>> *Alan N. Francis PhD*
>> Instructor - Imaging Neuroscience
>> Brain Imaging Center
>> McLean Hospital
>> Harvard Medical School
>> 115 Mill Street, Belmont, MA 02478
>> al...@bwh.harvard.edu
>> afran...@mclean.harvard.edu
>>
>>
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>
>
>
> --
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu
>
>
>
> --
> Jasmin Alves
> Predoctoral Student
> Medical Biology Graduate Program
> University of Southern California
> jal...@usc.edu
>
>
>


-- 
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

*Alan N. Francis PhD*
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478

[Freesurfer] Extract random effects for correlation

2016-04-13 Thread Lim Kai Wei, Joseph




Dear FS experts, 


I used the spatiotemporal LME to fit to my longitudinal data and performed some ad-hoc tests using the FDR2 correction. 


May I know how can I extract the random slopes characterizing individual variability in rate of change of cortical thickness at the significant vertices, and correlate them with my clinical and cognition scores? 


Thank you, 
Joseph




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