Re: [Freesurfer] Qdec-correction for multiple comparison

[John Anderson]

Hi Doug,

thank you veru much for the answr.

Please what do you mean by " an emperical question that depends on your data"? For example:

 

 I have two groups of participants. I ran cortical thickness analysis in Qdec to study the differnce between the groups in cortical thickness: 

1. Monte carlo simulation reported differnce between the groups ( p<0.05 ) in the precentral gyrus and the paracentral gyrus

2. FDR reported no diffwernce between the groups ( p<0.05)

 

Depending on pathology. I expect a differnce in the orecentral gyrus. How can I explain the results of FDR and mote carlo simulation? Does "empirical " means to follow the results that support the hypothesis?

 

 

 

John Anderson

Senior Research Associate
Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834
Fax: +1 (603) 646-1419

 
 

Sent: Wednesday, July 06, 2016 at 1:44 PM
From: "Douglas N Greve" 
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Qdec-correction for multiple comparison

There is no recommendation between FDR and monte carlo. The question of
which one is "better" is an emperical question that depends on your data.

On 06/29/2016 06:38 AM, John Anderson wrote:
> Dear FS experts,
> I will re post this thread again looking for your help and support:
> I ran cortical thickness analysis between two groups using Qdec and I
> want to correct the results for multiple comparison.
> In Qdec there are two choices to correct the data for multiple
> comparison (FDR and montecarlo) . Which method do you recommend to
> correct the results of cortical thickness analysis? Are there any
> rules that I need to follow when I choose my method to correct the
> results for multiple comparison ( i.e FDR or montecarlo)
> Thank you very much for any comment!
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>
>
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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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[Freesurfer] mri_segstats

[Alshikho, Mohamad J.]

Dear FS experts,
I have PET image "pet.anat.mgz" in subject space. I want to calculate the mean 
PET signal for every parcellate and segment in the atlas "wmparc.mgz".
Which one of the following commands is more accurate?


1.   mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab 
$FREESURFER_HOME/FREESURFERColorLUT.txt --i PET.anat.mgz --sum PET.wmparc.stats



2.   mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv 
mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/ 
PET.anat.mgz--in-intensity-name norm --in-intensity-units MR --subject ${subj} 
--surf-wm-vol --ctab /usr/local/freesurfer/stable5_3_0/WMParcStatsLUT.txt --etiv


Best,
Mohamad
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Re: [Freesurfer] question about exporting volumes

[Douglas N Greve]

what do you mean isolate? what do you mean export? You can create a 
binary mask in nifti format with mri_binarize --i aseg.mgz --match 10 49 
--o thalamus.mask.nii.gz


On 07/06/2016 04:46 PM, Dorsa Haji Ghaffari wrote:
>
>
>
> Hi,
>
> I was able to segment the MRI successfully, now I am trying to isolate 
> the thalamus and export it out of FS as a volume. Is there a way to do 
> that in FS?
>
> Thank you
>
> Dorsa
>
>
>
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-- 
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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_convert : ERROR: cannot unpack mosiacs without ASCII header

[Koubiyr, Ismail]

Hi,

This is a repost. Would anyone have a solution to this problem ?
Thanks for your help.

Best,

Ismail

> On Jul 5, 2016, at 11:24 AM, Koubiyr, Ismail  wrote:
> 
> The file has not been anonymized.
> 
> Thanks,
> 
> Ismail 
> 
>> On Jul 5, 2016, at 11:20 AM, Douglas N Greve  
>> wrote:
>> 
>> can you answer the question that it asks?
>> 
>> On 07/05/2016 10:52 AM, Koubiyr, Ismail wrote:
>>> Hi everyone,
>>> 
>>> I’m having some issues converting my DICOMs (DWI) into NIFTI using 
>>> mri_convert. I looked for other topics with people having the same 
>>> kind of problem but couldn’t find an answer.
>>> 
>>> Each time I run mri_convert on my DICOMs I get the following error :
>>> WARNING: file MR.1.3.12.2.1107.5.2.19.45306.2014091812330393354083931 
>>> does not contain a Siemens ASCII header
>>> has this file been anonymized?
>>> ERROR: cannot unpack mosiacs without ASCII header
>>> 
>>> Here are the following DICOMs informations :
>>> Identification
>>> NumarisVer   syngo MR D13
>>> ScannerModel Skyra
>>> PatientName   x
>>> Date and time
>>> StudyDate 20140918
>>> StudyTime 121037.203000
>>> SeriesTime   123450.60
>>> AcqTime   123257.367500
>>> Acquisition parameters
>>> PulseSeq ep_b0
>>> Protocol AX DTI no angle MS NEX 4 2
>>> PhEncDir COL
>>> EchoNo   1
>>> FlipAngle 90
>>> EchoTime 96
>>> InversionTime -1
>>> RepetitionTime   4700
>>> PhEncFOV 0
>>> ReadoutFOV   0
>>> Image information
>>> RunNo 4
>>> SeriesNo 5
>>> ImageNo   1
>>> NImageRows   990
>>> NImageCols   990
>>> NFrames   64
>>> SliceArraylSize   0
>>> IsMosaic 1
>>> ImgPos   1075.1575 1069.8385 -48.6769
>>> VolRes 2.1818   2.1818   2.
>>> VolDim 000
>>> Vc -1.  -0.   0.
>>> Vr -0.  -1.   0.
>>> Vs 0.   0.   0.
>>> VolCenter   0.   0.   0.
>>> TransferSyntaxUID 1.2.840.10008.1.2.1
>>> 
>>> 
>>> Then I try using mri_convert -it dicom, it converts the files but not 
>>> as it is expected, you could notice the difference when I run mri_info 
>>> on my output :
>>> Volume information for output.nii.gz
>>> type: nii
>>>   dimensions: 990 x 990 x 1 x 64
>>>  voxel sizes: 2.1818, 2.1818, 2.
>>> type: SHORT (4)
>>>  fov: 2160.000
>>>  dof: 0
>>>   xstart: -1080.0, xend: 1080.0
>>>   ystart: -1080.0, yend: 1080.0
>>>   zstart: -1.0, zend: 1.0
>>>   TR: 4700.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip 
>>> angle: 0.00 degrees
>>>  nframes: 64
>>>  PhEncDir: UNKNOWN
>>> ras xform present
>>>   xform info: x_r =  -1., y_r =  -0., z_r = -0., c_r =  
>>> -4.8425
>>> : x_a =  -0., y_a =  -1., z_a = -0., c_a =   
>>> -10.1615
>>> : x_s =   0., y_s =   0., z_s = 1., c_s =   
>>> -47.6769
>>> Orientation   : LPS
>>> Primary Slice Direction: axial
>>> 
>>> voxel to ras transform:
>>>  -2.1818  -0.  -0.  1075.1575
>>>  -0.  -2.1818  -0.  1069.8385
>>>   0.   0.   2.   -48.6769
>>>   0.   0.   0. 1.
>>> 
>>> voxel-to-ras determinant 9.52066
>>> 
>>> ras to voxel transform:
>>>  -0.4583   0.   0.   492.7805
>>>   0.  -0.4583   0.   490.3426
>>>  -0.  -0.   0.500024.3384
>>>   0.   0.   0. 1.
>>> 
>>> I would really appreciate your help, thank you.
>>> 
>>> Best,
>>> 
>>> Ismail
>>> 
>>> 
>>> 
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>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
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>> 
>> -- 
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>> 
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> 
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> 


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Re: [Freesurfer] fslaverage/MNI coordinates

[Li, Baojuan]

Hi Doug,

Thank you so much! Because I will do the analysis using SPM, I need the 
coordinates in MNI152 space. I found a transformation between them:

M = [0.9975   -0.00730.0176   -0.0429
   0.01461.0009   -0.00241.5496
  -0.0130   -0.00930.99711.1840
   000  1.]
Is this transformation correct? 
I guess I can then get the MNI152  coordinates in this way:
 
 P305 = [MNI305x MNI305y MNI305z 1]';
 P152 = M*P305 

Am I correct?

Best wishes,
Baojuan


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 06, 2016 4:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] fslaverage/MNI coordinates

Hi Baojuan, that coordinate will be mni305 space. Is that what you want?

On 07/06/2016 04:17 PM, Li, Baojuan wrote:
> Dear Freesurfer experts,
>
>
> I am using MNE (with MEG data) to define my ROIs for a connectivity
> analysis. I am going through the following steps to get the MNI
> coordinates of the regions:
>
> 1. Morph the subject's brain to fslaverage;
>
> 2. Load the inflated surface of fslaverage to MNE analyze;
>
> 3. Look for regions that are activated during my task;
>
> 3. Use view>show coordinates to show the coordinates of the vertex;
>
> 4. The surface RAS (MRI) coordinates are shown;
>
> 5. Used these coordinates as MNI coordinates.
>
> Because I was using SPM in the past and am quite new to freesurfer, I
> strongly hope someone can help me to check if I have done it
> correctly. Thank you so much for your help!
>
> Best wishes,
> Baojuan
>
>
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--
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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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[Freesurfer] question about exporting volumes

[Dorsa Haji Ghaffari]

Hi,

I was able to segment the MRI successfully, now I am trying to isolate the
thalamus and export it out of FS as a volume. Is there a way to do that in
FS?

Thank you

Dorsa
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Re: [Freesurfer] fslaverage/MNI coordinates

[Douglas N Greve]

Hi Baojuan, that coordinate will be mni305 space. Is that what you want?

On 07/06/2016 04:17 PM, Li, Baojuan wrote:
> Dear Freesurfer experts,
>
>
> I am using MNE (with MEG data) to define my ROIs for a connectivity 
> analysis. I am going through the following steps to get the MNI 
> coordinates of the regions:
>
> 1. Morph the subject's brain to fslaverage;
>
> 2. Load the inflated surface of fslaverage to MNE analyze;
>
> 3. Look for regions that are activated during my task;
>
> 3. Use view>show coordinates to show the coordinates of the vertex;
>
> 4. The surface RAS (MRI) coordinates are shown;
>
> 5. Used these coordinates as MNI coordinates.
>
> Because I was using SPM in the past and am quite new to freesurfer, I 
> strongly hope someone can help me to check if I have done it 
> correctly. Thank you so much for your help!
>
> Best wishes,
> Baojuan
>
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] fslaverage/MNI coordinates

[Li, Baojuan]

Dear Freesurfer experts,


I am using MNE (with MEG data) to define my ROIs for a connectivity analysis. I 
am going through the following steps to get the MNI coordinates of the regions:

1. Morph the subject's brain to fslaverage;

2. Load the inflated surface of fslaverage to MNE analyze;

3. Look for regions that are activated during my task;

3. Use view>show coordinates to show the coordinates of the vertex;

4. The surface RAS (MRI) coordinates are shown;

5. Used these coordinates as MNI coordinates.

Because I was using SPM in the past and am quite new to freesurfer, I strongly 
hope someone can help me to check if I have done it correctly. Thank you so 
much for your help!

Best wishes,
Baojuan
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Re: [Freesurfer] question about white matter edits

[Bruce Fischl]

Hi Rito

the control points you have look like they are in voxels that contain 
some gray matter, which will probably make things worse. YOu need to 
identify why you are missing that part of the surface. Is the dark stuff 
there labeled as white? Maybe it's a topological defect that gets filled 
incorrectly?

cheers
Bruce


On Wed, 6 Jul 2016, Ritobrato Datta wrote:

> Hi All,
>
> We have run recon-all on T1 FLASH images have identified regions where the 
> sulci were included inside the white matter boundary. We added controls 
> points around the sulci (please see attached pic) and reran recon-all as 
> follows
>
> recon-all -autorecon2-cp -autorecon3 -subjid 
>
> but on a lot of instances, the specified control points were not incorporated 
> (please see attached image). How do we fix this, now that we have already run 
> the recon-all with -autorecon2-cp and the error persists ?
>
> Can someone please suggest ?
>
> Thank you,
>
> Rito and Jack
>
>
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[Freesurfer] Design Matrix Creation

[Timothy Hendrickson]

Hi Doug,

I just wanted to make sure that we were on the same page. I may have
been a little unclear in what I would ideally like to do.

For #2 what I would like to do is take into account age slopes and
total intracranial slopes for gender, and age slopes and total
intracranial slopes for diagnosis.
I was not implying that I wanted diagnosis and gender to interact.

Assuming that you understood this previously could you please explain
why you would model the matrix this way? I do not fully understand.

Respectfully,

-Tim


>I did not get the same matrix. Here's how I would do it
>Columns 1-16 model the intercepts for all your classes
>Columns 17-20 model the ages for your gender-x-diagnosis subclasses
>Columns 21-24 model the ICV for your gender-x-diagnosis subclasses

On 07/06/2016 02:04 PM, Timothy Hendrickson wrote:
> Freesurfer Support,
>
> Thank you for your support with my previous line of questions regarding
> design matrix creation.
> I have manually created another design matrix and want to ensure that I
> designed it correctly.
>
> An example of my FSGD file is as follows below:
> Class SITE 1-Male-Control
> Class SITE 1-Male-PATIENT
> Class SITE 1-Female-Control
> Class SITE 1-Female-PATIENT
> Class SITE 2-Male-Control
> Class SITE 2-Male-PATIENT
> Class SITE 2-Female-Control
> Class SITE 2-Female-PATIENT
> Class SITE 3-Male-Control
> Class SITE 3-Male-PATIENT
> Class SITE 3-Female-Control
> Class SITE 3-Female-PATIENT
> Class SITE 4-Male-Control
> Class SITE 4-Male-PATIENT
> Class SITE 4-Female-Control
> Class SITE 4-Female-PATIENT
> Variables age_at_scan total_intracranial_volume
> study site levels = 1, 2, 3, 4
> gender levels = Male, Female
> diagnosis levels = PATIENT, Control
> age_at_scan = covariate age
> total_intracranial_volume = covariate total intracranial volume
>
> What I would ideally like to do is:
>
> 1) Take into account offset differences amongst diagnosis, gender, and study
> site.
>
> 2) Allowing a difference in age slope, and total intracranial volume slope
> amongst the diagnosis and gender levels.
>
> 3) Modeling the age slope and total intracranial volume slope as the same for
> the study site levels.
> Let's image that the first participant is from site 1, Male, and control, and
> is 12 and has a TIV of 30,000.
> The second participant is from site 2, Female, and PATIENT, and is 14, and
> has a TIV of 25,000.
> My understanding of the design matrix would be as follows:
> 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 3 0 0 0
> 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 25000
> -Tim
>
> >Yes, create your matrix manually.
> >
> >Those matrix lines are not quite right. The ages are in the correct
> >column, but you need a 1 somewhere in columns 1-8 to indicate the class
> >(ie, site/dx) that the subject is in.
> On 05/26/2016 12:57 PM, Timothy Hendrickson wrote:
> > Hi Doug,
> >
> > Thank you for such a prompt response. Just to be clear you are
> > recommending that I manually create the matrix file right?
> >
> > If so I want to ensure that I am understanding how to design the
> > matrix file properly.
> >
> > Let's imagine that the first participant is a control and is 13 and
> > the second is a patient and is 15. My understanding is that the matrix
> > file would be as follows:
> > 0 0 0 0 0 0 0 0 13 0
> > 0 0 0 0 0 0 0 0 0 15.
> >
> > -Tim
> > Previous correspondences are below:
> >
> > You'll need a regressor for each of the 8 classes you describe below.
> > You can use mri_glmfit to generate this (Xg.dat file)
> > You'll need two more regressors for age, one for each diagnosis. If a
> > subject (ie, row) is a control then the two values will be AGE 0. If the
> > subject of the row is a patient, then the two values will be 0 AGE. You
> > can then set up a Controls-Patients age (ie, interaction between dx and
> > age) contrast like
> > [0 0 0 0 0 0 0 0 1 -1]
> > On 05/24/2016 02:30 PM, Timothy Hendrickson wrote:
> > >
> > > Freesurfer Support,
> > >
> > > I'd like to create a design matrix for a group analysis outside of the
> > > DODS and DOSS models. I understand that in order to do this the -X
> > > flag must be used. However, I have been unable to find examples of how
> > > to do this.
> > >
> > > I am hoping to reveal a difference in thickness or gyrification
> > > amongst a clinical population. The data set contains two factors:
> > > diagnosis, and study site and one covariate: age. Diagnosis has two
> > > levels: controls, and patients. Study site has four levels, one level
> > > for each location the data has been collected from.
> > >
> > > What I would ideally like to do is:
> > >
> > > 1) Take into account offset differences amongst diagnosis and study site.
> > >
> > > 2) Allowing a difference in age slope amongst the diagnosis levels
> > >
> > > 3) Modeling the age slope as the same for the study site levels
> > >
> > > My FSGD file is designed as follows
> > >
> > > Class SITE 1-Control
> > > Class SITE 1-PATIENT
> > > Class SITE 2-Control
> > > 

Re: [Freesurfer] question about white matter edits

[Harms, Michael]

Hi,
The missing sulcus may be a consequence of the topology correction going awry.  Check the “nofix” surface to see the surface before topology correction.  If the topology correction is the problem, you’ll need to edit the wm.mgz.  There is an example on
 the FS tutorials.


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  63110 
Email: mha...@wustl.edu







From:  on behalf of Barbara Kreilkamp 
Reply-To: Freesurfer support list 
Date: Wednesday, July 6, 2016 at 12:05 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] question about white matter edits





Hi Rito,
I just read this today myself "Select a few control points around your trouble areas, space them out throughout the brain and on different slices. You want to pick points in a region where the wm intensity is lower than it should be (that is, having a voxel
 value less than 110)." from 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview

Could it be that those control points grasp voxels that already have an intensity of at least 110? 
Best wishes,
Barbara





On 06/07/2016 17:25, Ritobrato Datta wrote:


Hi All,

We have run recon-all on T1 FLASH images have identified regions where the sulci were included inside the white matter boundary. We added controls points around the sulci (please see attached pic) and reran recon-all as follows

recon-all -autorecon2-cp -autorecon3 -subjid 

but on a lot of instances, the specified control points were not incorporated (please see attached image). How do we fix this, now that we have already run the recon-all with -autorecon2-cp and the error persists ?

Can someone please suggest ?

Thank you,

Rito and Jack



 
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[Freesurfer] LGI Summary Statistics

[Timothy Hendrickson]

Freesurfer Support,

I have seen previous message threads on extracting LGI measurements across
ROIs, however I have yet to find anything which would provide a summary LGI
across an entire hemsphere.
Other measurements like cortical thickness have a measurement like this. Is
there a measurement like this for LGI?

If I take the mean of all of the ROIs would that be equivalent to a
hemispheric LGI measure?

Thanks!

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Mobile: 507-259-3434 (texts okay)
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Re: [Freesurfer] Seed based volume output to surface

[Douglas N Greve]

The output L_parahipp_seed.surf.lh/L_parahipp/sig.nii.gz is already on 
the surface.
if you need the output as text, you can run mri_convert sig.nii.gz 
output.txt --ascii
or use --ascii+crsf


--ascii
 save output as ascii. This will be a data file with a 
single
 column of data. The fastest dimension will be col, then
 row,then slice, then frame.
--ascii+crsf
 same as --ascii but includes col row slice and frame




On 06/30/2016 05:42 PM, Taha Abdullah wrote:
> Good Afternoon Freesurfers,
>
> I am running a seed-based connectivity for one individual subject. The 
> seed is in the L_parahippocampus. I have followed the steps outlined 
> in FSFast walkthrough. Below is a list of my commands. Mind you that I 
> was trying to keep my analysis as simple as possible before delving 
> deeper into it. I have a question on the sig.nii.gz output. Please see 
> at the end.
>
> preproc-sess -s taha_brain -fwhm 0 -surface self lhrh -mni305-2mm -fsd 
> resting_scans -per-run
>
> fcseed-config -segid 1016 -fcname L_parahipp -fsd resting_scans -mean 
> -cfg mean.L_parahipp.config -overwrite -fillthresh 1
>
> fcseed-sess -s taha_brain -cfg mean.L_parahipp.config
>
> mkanalysis-sess -analysis L_parahipp_seed.surf.lh -surface self lh 
> -fwhm 0 -notask -taskreg L_parahipp 1 -fsd resting_scans -TR 0.555 
> -mcextreg -polyfit 2 -per-run
>
> selxavg3-sess -s taha_brain -a L_parahipp_seed.surf.lh
>
> Output files 
> /home/tabdullah/Project/Sess01/fsd/L_parahipp_seed.surf.lh/L_parahipp/sig.nii.gz
> amongst others
>
> *Is there a way to convert the volume to a surface and then extract 
> per vertex the sig value?* I used tmri_vol2surf see below:
>
> mri_vol2surf --mov ./sig.nii.gz --reg 
> /home/tabdullah/resting_state_1/taha_brain/resting_scans/001/register.dof6.dat
>  
> --trgsubject taha_brain --interp nearest --projfrac 0.5 --hemi lh --o 
> /home/tabdullah/sig.mgh --noreshape --cortex
>
> I tried using mris_convert -c
>
> mris_convert -c ./sig.mgh 
> /usr/local/freesurfer/subjects/taha_brain/surf/lh.white sig.asc
>
> The last column is all zeros. I am not entirely sure what I am doing 
> wrong here, it is probably somewhere in the last two commands. 
> Possibly using mri_segstats or mri_read.m? Any help would be greatly 
> appreciated. Apologize in advance for the long email.
>
>
> -- 
> Taha Abdullah
> Department of Physiology
> Northwestern University Feinberg School of Medicine
> Masters of Science Physiology and Biophysics, Georgetown University 2015
> Work: (312)-503-0413
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
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Re: [Freesurfer] Design Matrix Creation

[Douglas N Greve]

I did not get the same matrix. Here's how I would do it
Columns 1-16 model the intercepts for all your classes
Columns 17-20 model the ages for your gender-x-diagnosis subclasses
Columns 21-24 model the ICV for your gender-x-diagnosis subclasses


On 07/06/2016 02:04 PM, Timothy Hendrickson wrote:
> Freesurfer Support,
>
> Thank you for your support with my previous line of questions regarding 
> design matrix creation.
> I have manually created another design matrix and want to ensure that I 
> designed it correctly.
>
> An example of my FSGD file is as follows below:
> Class SITE 1-Male-Control
> Class SITE 1-Male-PATIENT
> Class SITE 1-Female-Control
> Class SITE 1-Female-PATIENT
> Class SITE 2-Male-Control
> Class SITE 2-Male-PATIENT
> Class SITE 2-Female-Control
> Class SITE 2-Female-PATIENT
> Class SITE 3-Male-Control
> Class SITE 3-Male-PATIENT
> Class SITE 3-Female-Control
> Class SITE 3-Female-PATIENT
> Class SITE 4-Male-Control
> Class SITE 4-Male-PATIENT
> Class SITE 4-Female-Control
> Class SITE 4-Female-PATIENT
> Variables age_at_scan total_intracranial_volume
> study site levels = 1, 2, 3, 4
> gender levels = Male, Female
> diagnosis levels = PATIENT, Control
> age_at_scan = covariate age
> total_intracranial_volume = covariate total intracranial volume
>
> What I would ideally like to do is:
>
> 1) Take into account offset differences amongst diagnosis, gender, and study 
> site.
>
> 2) Allowing a difference in age slope, and total intracranial volume slope 
> amongst the diagnosis and gender levels.
>
> 3) Modeling the age slope and total intracranial volume slope as the same for 
> the study site levels.
> Let's image that the first participant is from site 1, Male, and control, and 
> is 12 and has a TIV of 30,000.
> The second participant is from site 2, Female, and PATIENT, and is 14, and 
> has a TIV of 25,000.
> My understanding of the design matrix would be as follows:
> 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 3 0 0 0
> 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 25000
> -Tim
>
> >Yes, create your matrix manually.
> >
> >Those matrix lines are not quite right. The ages are in the correct
> >column, but you need a 1 somewhere in columns 1-8 to indicate the class
> >(ie, site/dx) that the subject is in.
> On 05/26/2016 12:57 PM, Timothy Hendrickson wrote:
> > Hi Doug,
> >
> > Thank you for such a prompt response. Just to be clear you are
> > recommending that I manually create the matrix file right?
> >
> > If so I want to ensure that I am understanding how to design the
> > matrix file properly.
> >
> > Let's imagine that the first participant is a control and is 13 and
> > the second is a patient and is 15. My understanding is that the matrix
> > file would be as follows:
> > 0 0 0 0 0 0 0 0 13 0
> > 0 0 0 0 0 0 0 0 0 15.
> >
> > -Tim
> > Previous correspondences are below:
> >
> > You'll need a regressor for each of the 8 classes you describe below.
> > You can use mri_glmfit to generate this (Xg.dat file)
> > You'll need two more regressors for age, one for each diagnosis. If a
> > subject (ie, row) is a control then the two values will be AGE 0. If the
> > subject of the row is a patient, then the two values will be 0 AGE. You
> > can then set up a Controls-Patients age (ie, interaction between dx and
> > age) contrast like
> > [0 0 0 0 0 0 0 0 1 -1]
> > On 05/24/2016 02:30 PM, Timothy Hendrickson wrote:
> > >
> > > Freesurfer Support,
> > >
> > > I'd like to create a design matrix for a group analysis outside of the
> > > DODS and DOSS models. I understand that in order to do this the -X
> > > flag must be used. However, I have been unable to find examples of how
> > > to do this.
> > >
> > > I am hoping to reveal a difference in thickness or gyrification
> > > amongst a clinical population. The data set contains two factors:
> > > diagnosis, and study site and one covariate: age. Diagnosis has two
> > > levels: controls, and patients. Study site has four levels, one level
> > > for each location the data has been collected from.
> > >
> > > What I would ideally like to do is:
> > >
> > > 1) Take into account offset differences amongst diagnosis and study site.
> > >
> > > 2) Allowing a difference in age slope amongst the diagnosis levels
> > >
> > > 3) Modeling the age slope as the same for the study site levels
> > >
> > > My FSGD file is designed as follows
> > >
> > > Class SITE 1-Control
> > > Class SITE 1-PATIENT
> > > Class SITE 2-Control
> > > Class SITE 2-PATIENT
> > > Class SITE 3-Control
> > > Class SITE 3-PATIENT
> > > Class SITE 4-Control
> > > Class SITE 4-PATIENT
> > > Variables age_at_scan
> > >
> > > study site levels = 1,2,3 and 4
> > > diagnosis levels = PATIENT and Control
> > > age_at_scan = covariate age
> > >
> > > Any advice would be greatly appreciated.
> > >
> > > Respectfully,
> > >
> > > Tim
> > >
> > > --
> > > Timothy Hendrickson
> > > Department of Psychiatry
> > > University of Minnesota
> > > Mobile: 507-259-3434  (texts okay)
>
>
> 

Re: [Freesurfer] mris_preproc subject-volume mismatch

[Douglas N Greve]

Ah, the problem is with using an lta with 5.3 mris_preproc. I've put 
version 6 mris_preproc here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc
try that and see if it works. Alternatively, you could convert the lta 
files to register.dat files


On 07/06/2016 02:02 PM, Raney, Talia L. wrote:
> Hmm, it says that there is one frame in each of the subjects.
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, July 06, 2016 1:54 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
>
> It must be that one of the ces files has multiple frames. Try running
> mri_info --nframes ces.nii.gz
> on all of the ces files to see how many frames are in each
>
> On 07/06/2016 01:39 PM, Raney, Talia L. wrote:
>> mris_preproc --target fsaverage --hemi lh --iv 
>> WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz 
>> WADG77j/restingstate/bb.register.lta --iv 
>> WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz 
>> WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh
>> ERROR: number of input volumes (2) does not equal number of subjects (8)
>> It apparently thinks one volume is 4 subjects but when checking 
>> bb.register.lta, it doesn't appear to be the case.
>> Thanks!
>> Talia
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
>> [gr...@nmr.mgh.harvard.edu]
>> Sent: Wednesday, July 06, 2016 1:19 PM
>> To: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
>>
>> can you send the terminal output?
>>
>> On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
>>> Hi FreeSurfer users,
>>> I'm trying to use mri-preproc to do a group fMRI analysis(based on the 
>>> tutorial). However, I keep getting an error that the number of input 
>>> volumes does not equal number of subjects. It seems one volume is counted 
>>> as 4 subjects. I'm wondering what the command determines to be the subject 
>>> list when you use the --iv flag.
>>> For reference, I'm basing it off of this command:
>>> mris_preproc --target fsaverage --hemi lh \
>>>  --iv  fbirn-101/ces.nii fbirn-101/bb.register.lta \
>>>  --iv  fbirn-103/ces.nii fbirn-103/bb.register.lta \
>>>  --iv  fbirn-104/ces.nii fbirn-104/bb.register.lta \
>>>  --iv  fbirn-105/ces.nii fbirn-105/bb.register.lta \
>>>  --iv  fbirn-106/ces.nii fbirn-106/bb.register.lta \
>>>  --projfrac 0.5 \
>>>  --out lh.ces.mgh
>>> Thanks!
>>> Talia
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
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>> ___
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>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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The information in this e-mail is intended only for the person to 

[Freesurfer] Design Matrix Creation

[Timothy Hendrickson]

Freesurfer Support,

Thank you for your support with my previous line of questions
regarding design matrix creation.
I have manually created another design matrix and want to ensure that
I designed it correctly.

An example of my FSGD file is as follows below:
Class SITE 1-Male-Control
Class SITE 1-Male-PATIENT
Class SITE 1-Female-Control
Class SITE 1-Female-PATIENT
Class SITE 2-Male-Control
Class SITE 2-Male-PATIENT
Class SITE 2-Female-Control
Class SITE 2-Female-PATIENT
Class SITE 3-Male-Control
Class SITE 3-Male-PATIENT
Class SITE 3-Female-Control
Class SITE 3-Female-PATIENT
Class SITE 4-Male-Control
Class SITE 4-Male-PATIENT
Class SITE 4-Female-Control
Class SITE 4-Female-PATIENT
Variables age_at_scan total_intracranial_volume

study site levels = 1, 2, 3, 4

gender levels = Male, Female

diagnosis levels = PATIENT, Control

age_at_scan = covariate age

total_intracranial_volume = covariate total intracranial volume

What I would ideally like to do is:
1) Take into account offset differences amongst diagnosis, gender, and
study site.
2) Allowing a difference in age slope, and total intracranial volume
slope amongst the diagnosis and gender levels.

3) Modeling the age slope and total intracranial volume slope as the
same for the study site levels.

Let's image that the first participant is from site 1, Male, and
control, and is 12 and has a TIV of 30,000.
The second participant is from site 2, Female, and PATIENT, and is 14,
and has a TIV of 25,000.

My understanding of the design matrix would be as follows:
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 3 0 0 0
0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 25000

-Tim



>Yes, create your matrix manually.
>
>Those matrix lines are not quite right. The ages are in the correct
>column, but you need a 1 somewhere in columns 1-8 to indicate the class
>(ie, site/dx) that the subject is in.

On 05/26/2016 12:57 PM, Timothy Hendrickson wrote:
> Hi Doug,
>
> Thank you for such a prompt response. Just to be clear you are
> recommending that I manually create the matrix file right?
>
> If so I want to ensure that I am understanding how to design the
> matrix file properly.
>
> Let's imagine that the first participant is a control and is 13 and
> the second is a patient and is 15. My understanding is that the matrix
> file would be as follows:
> 0 0 0 0 0 0 0 0 13 0
> 0 0 0 0 0 0 0 0 0 15.
>
> -Tim
> Previous correspondences are below:
>
> You'll need a regressor for each of the 8 classes you describe below.
> You can use mri_glmfit to generate this (Xg.dat file)
> You'll need two more regressors for age, one for each diagnosis. If a
> subject (ie, row) is a control then the two values will be AGE 0. If the
> subject of the row is a patient, then the two values will be 0 AGE. You
> can then set up a Controls-Patients age (ie, interaction between dx and
> age) contrast like
> [0 0 0 0 0 0 0 0 1 -1]
> On 05/24/2016 02:30 PM, Timothy Hendrickson wrote:
> >
> > Freesurfer Support,
> >
> > I'd like to create a design matrix for a group analysis outside of the
> > DODS and DOSS models. I understand that in order to do this the -X
> > flag must be used. However, I have been unable to find examples of how
> > to do this.
> >
> > I am hoping to reveal a difference in thickness or gyrification
> > amongst a clinical population. The data set contains two factors:
> > diagnosis, and study site and one covariate: age. Diagnosis has two
> > levels: controls, and patients. Study site has four levels, one level
> > for each location the data has been collected from.
> >
> > What I would ideally like to do is:
> >
> > 1) Take into account offset differences amongst diagnosis and study site.
> >
> > 2) Allowing a difference in age slope amongst the diagnosis levels
> >
> > 3) Modeling the age slope as the same for the study site levels
> >
> > My FSGD file is designed as follows
> >
> > Class SITE 1-Control
> > Class SITE 1-PATIENT
> > Class SITE 2-Control
> > Class SITE 2-PATIENT
> > Class SITE 3-Control
> > Class SITE 3-PATIENT
> > Class SITE 4-Control
> > Class SITE 4-PATIENT
> > Variables age_at_scan
> >
> > study site levels = 1,2,3 and 4
> > diagnosis levels = PATIENT and Control
> > age_at_scan = covariate age
> >
> > Any advice would be greatly appreciated.
> >
> > Respectfully,
> >
> > Tim
> >
> > --
> > Timothy Hendrickson
> > Department of Psychiatry
> > University of Minnesota
> > Mobile: 507-259-3434  (texts okay)
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Re: [Freesurfer] FSFAST- Cerebellum

[Douglas N Greve]

What is the problem with the orientation? The little letters indicate 
that the orientation is correct. fslview ignores the orientation when 
displaying so it might come out upside down.

On 07/05/2016 01:35 PM, Sabin Khadka wrote:
>
> Hi Doug, As you suggested I mapped fmri into the anatomical space using
>
> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o 
> fmcpr.anat.nii.gz
>
> The orientation of fmcpr.anat.nii.gz seem to have some problem (see 
> below). However the label seems to be correct. I am a bit confused 
> here. Do I need to tranform the file somehow?
>
> fmcpr.nii.gz
>
> Inline image 1
>
> fmcpr.anat.nii.gz
>
> Inline image 2
>
>
>
> Cheers,
> Sabin Khadka
>
> On Thu, Jun 23, 2016 at 11:28 AM, Douglas Greve 
> > wrote:
>
> After you run preproc-sess, there will be a file called
> register.dof6.dat. Map fmri into the anatomical space, something like
>
> mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat
> --o fmcpr.anat.nii.gz
>
> Then use mri_segstats with --seg aseg.mgz --i fmcpr.anat.nii.gz
>
> However, I don't think that the aseg has those cerebellum
> parcellations.
>
> On 6/21/16 5:52 PM, Sabin Khadka wrote:
>> Hi Yeo- Thanks very much for your answer. Yes the data is in
>> mni305 space. I process my fmri data with
>>
>> preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
>> -fwhm 6 -per-run -stc odd
>> and then to extract ROI time series values I did
>>
>> mri_segstats --annot fsaverage rh aparc --i
>> rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid
>> 2000 --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>>
>> and for cortical time series
>>
>> mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
>> /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12
>> --id 13 --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52
>> --id 53 --id 54 --id 58 --i
>> rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
>> subCorticalTimeSeries.txt
>>
>> Now I am not sure as how to extract cerebellum ROIs (time series
>> as described in Buckner et.al  2011)? If there are
>> any other additional steps I need to perform ? or if I have to
>> use some other scripts commands (other than mri_segstats).
>>
>>
>> Cheers,
>> Sabin Khadka
>>
>> On Mon, Jun 20, 2016 at 10:20 PM, Thomas Yeo
>> > wrote:
>>
>> Hi Sabin,
>>
>> The structures 601-628 FreeSurferCololLUT.txt correspond to
>> anatomical
>> substructures of the cerebellum (e.g., Crus I, etc). Is that
>> what you
>> want? Or are you looking to use the functional parcels defined in
>> Buckner 2011?
>>
>> In addition, I do not know how mri_segstats works, so I
>> cannot verify
>> how you call the command is correct. Maybe others can provide
>> feedback
>> here.
>>
>> However, the Buckner cerebellar parcellations in
>> $FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/ is
>> in MNI152
>> space. From your command, I assume your data is in MNI305
>> space. So
>> you might need to transform the parcellation from MNI152 to
>> MNI305.
>>
>> Thanks,
>> Thomas
>>
>> On Sat, Jun 18, 2016 at 8:49 AM, Sabin Khadka
>> >
>> wrote:
>> > Hi all,
>> >
>> > I am trying to extract mean time series BOLD data using
>> FSFAST from Cortical
>> > ROIs + sub cortical ROIs and cerebellum.
>> >
>> > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh
>> -mni305 -fwhm 6
>> > -per-run -stc oddmri_segstats --annot fsaverage lh
>> aparc --i
>> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz
>> --excludeid 1000
>> > --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
>> > mri_segstats --annot fsaverage rh aparc --i
>> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz
>> --excludeid 2000
>> > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
>> >
>> > and for cortical time series
>> >
>> > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
>> > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id
>> 12 --id 13 --id
>> > 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53
>> --id 54 --id 58
>> > --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz --avgwf
>> > subCorticalTimeSeries.txt
>> >
>> > But I am not sure on how exactly to extract time series
>> from cerebellar
>> > regions. So if I want to extract time series from regions
>> 

Re: [Freesurfer] mris_preproc subject-volume mismatch

[Raney, Talia L.]

Hmm, it says that there is one frame in each of the subjects. 

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 06, 2016 1:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch

It must be that one of the ces files has multiple frames. Try running
mri_info --nframes ces.nii.gz
on all of the ces files to see how many frames are in each

On 07/06/2016 01:39 PM, Raney, Talia L. wrote:
> mris_preproc --target fsaverage --hemi lh --iv 
> WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz 
> WADG77j/restingstate/bb.register.lta --iv 
> WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz 
> WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh
> ERROR: number of input volumes (2) does not equal number of subjects (8)
> It apparently thinks one volume is 4 subjects but when checking 
> bb.register.lta, it doesn't appear to be the case.
> Thanks!
> Talia
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, July 06, 2016 1:19 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
>
> can you send the terminal output?
>
> On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
>> Hi FreeSurfer users,
>> I'm trying to use mri-preproc to do a group fMRI analysis(based on the 
>> tutorial). However, I keep getting an error that the number of input volumes 
>> does not equal number of subjects. It seems one volume is counted as 4 
>> subjects. I'm wondering what the command determines to be the subject list 
>> when you use the --iv flag.
>> For reference, I'm basing it off of this command:
>> mris_preproc --target fsaverage --hemi lh \
>> --iv  fbirn-101/ces.nii fbirn-101/bb.register.lta \
>> --iv  fbirn-103/ces.nii fbirn-103/bb.register.lta \
>> --iv  fbirn-104/ces.nii fbirn-104/bb.register.lta \
>> --iv  fbirn-105/ces.nii fbirn-105/bb.register.lta \
>> --iv  fbirn-106/ces.nii fbirn-106/bb.register.lta \
>> --projfrac 0.5 \
>> --out lh.ces.mgh
>> Thanks!
>> Talia
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Intensity stats question

[Douglas N Greve]

that looks right. You might want to call the output something else so 
that you don't overwrite the default FS output

On 07/06/2016 01:55 PM, Sabrina Yu wrote:
>
> Hi,
>
>
> Thanks for the quick reply. I just want to confirm that my command is 
> correct for changing the input volume to orig.mgz:
>
>
> mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv 
> mri/orig.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in 
> mri/orig.mgz --in-intensity-name orig --in-intensity-units MR 
> --subject SUBJECT --surf-wm-vol --ctab 
> /Applications/freesurfer/WMParcStatsLUT.txt --etiv
>
>
> Thanks
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Douglas N Greve 
> 
> *Sent:* Wednesday, July 6, 2016 10:21:41 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Intensity stats question
>
>
> On 07/06/2016 01:05 PM, Sabrina Yu wrote:
> >
> > Hello,
> >
> >
> > I have a couple of questions about the wmparc.stats file generated.
> > What volume is the data based on?
> >
> norm.mgz
> >
> > Has the intensity of the volume been corrected?
> >
> Yes
> >
> > I just need the average voxel intensity over the ROIs, but am unsure
> > if this intensity is based on an intensity normalized brain volume.
> >
> >
> > Is it possible to change the input volume for wmparc.stats to orig.mgz?
> >
> Look in the subject/scripts/recon-all.log file for the mri_segstats
> command that generates the wmparc.stats file
> >
> >
> > Thank you in advance.
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
> 
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom 
> it is
> addressed. If you believe this e-mail was sent to you in error and the 
> e-mail
> contains patient information, please contact the Partners Compliance 
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you 
> in error
> but does not contain patient information, please contact the sender 
> and properly
> dispose of the e-mail.
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] Intensity stats question

[Sabrina Yu]

Hi,


Thanks for the quick reply. I just want to confirm that my command is correct 
for changing the input volume to orig.mgz:


mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/orig.mgz 
--excludeid 0 --brainmask mri/brainmask.mgz --in mri/orig.mgz 
--in-intensity-name orig --in-intensity-units MR --subject SUBJECT 
--surf-wm-vol --ctab /Applications/freesurfer/WMParcStatsLUT.txt --etiv


Thanks


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

Sent: Wednesday, July 6, 2016 10:21:41 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Intensity stats question



On 07/06/2016 01:05 PM, Sabrina Yu wrote:
>
> Hello,
>
>
> I have a couple of questions about the wmparc.stats file generated.
> What volume is the data based on?
>
norm.mgz
>
> Has the intensity of the volume been corrected?
>
Yes
>
> I just need the average voxel intensity over the ROIs, but am unsure
> if this intensity is based on an intensity normalized brain volume.
>
>
> Is it possible to change the input volume for wmparc.stats to orig.mgz?
>
Look in the subject/scripts/recon-all.log file for the mri_segstats
command that generates the wmparc.stats file
>
>
> Thank you in advance.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] mris_preproc subject-volume mismatch

[Douglas N Greve]

It must be that one of the ces files has multiple frames. Try running
mri_info --nframes ces.nii.gz
on all of the ces files to see how many frames are in each

On 07/06/2016 01:39 PM, Raney, Talia L. wrote:
> mris_preproc --target fsaverage --hemi lh --iv 
> WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz 
> WADG77j/restingstate/bb.register.lta --iv 
> WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz 
> WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh
> ERROR: number of input volumes (2) does not equal number of subjects (8)
> It apparently thinks one volume is 4 subjects but when checking 
> bb.register.lta, it doesn't appear to be the case.
> Thanks!
> Talia
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
> [gr...@nmr.mgh.harvard.edu]
> Sent: Wednesday, July 06, 2016 1:19 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch
>
> can you send the terminal output?
>
> On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
>> Hi FreeSurfer users,
>> I'm trying to use mri-preproc to do a group fMRI analysis(based on the 
>> tutorial). However, I keep getting an error that the number of input volumes 
>> does not equal number of subjects. It seems one volume is counted as 4 
>> subjects. I'm wondering what the command determines to be the subject list 
>> when you use the --iv flag.
>> For reference, I'm basing it off of this command:
>> mris_preproc --target fsaverage --hemi lh \
>> --iv  fbirn-101/ces.nii fbirn-101/bb.register.lta \
>> --iv  fbirn-103/ces.nii fbirn-103/bb.register.lta \
>> --iv  fbirn-104/ces.nii fbirn-104/bb.register.lta \
>> --iv  fbirn-105/ces.nii fbirn-105/bb.register.lta \
>> --iv  fbirn-106/ces.nii fbirn-106/bb.register.lta \
>> --projfrac 0.5 \
>> --out lh.ces.mgh
>> Thanks!
>> Talia
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] mapping a surface from fsaverage_sym to the subject's native surface

[Douglas N Greve]

It would be something like
mris_apply_reg --src lh.data-from-fsavgsym.mgh --streg 
$SUBJECTS_DIR/fsaverage_sym/surf/lh.sphere.reg 
$SUBJECTS_DIR/yoursubject/surf/lh.fsaverage_sym.sphere.reg --o 
lh.data-from-fsavgsym-on-yoursubject.mgh


On 07/04/2016 10:34 AM, Ali-Reza Mohammadi-Nejad wrote:
> Dear Freesurfer experts,
>
> Based on the FS wiki, I calculated the cortical thickness difference 
> between the lh and rh of a subject.
> Now, I want to use the “mris_apply_reg” command to map the “left-right 
>  difference” from fsaverage_sym back to the subject's native surface.
> Unfortunately, I did not find the appropriate options of this command 
> to do this work.
> Thanks for any help.
> Best regards,
> Ali-Reza
> Ali-Reza Mohammadi-Nejad
> Pre-doctoral research fellow
> Radiology and Neurology Research
> Henry Ford Health System
> Detroit, MI 48202, USA
>
>
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-- 
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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] Qdec-correction for multiple comparison

[Douglas N Greve]

There is no recommendation between FDR and monte carlo. The question of 
which one is "better" is an emperical question that depends on your data.

On 06/29/2016 06:38 AM, John Anderson wrote:
> Dear FS experts,
> I will re post this thread again looking for your help and support:
> I ran cortical thickness analysis between two groups using Qdec and I 
> want to correct the results for multiple comparison.
> In Qdec there are two choices to correct the data for multiple 
> comparison (FDR and montecarlo) . Which method do you recommend to 
> correct the results of cortical thickness analysis? Are there any 
> rules that I need to follow when I choose my method to correct the 
> results for multiple comparison ( i.e FDR or montecarlo)
> Thank you very much for any comment!
> John Anderson
>
> Senior Research Associate
> Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834
> Fax: +1 (603) 646-1419
>
>
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Re: [Freesurfer] Applying the lta transformation to PET image | mri_coreg | mri_segstats

[Douglas N Greve]

use mri_vol2vol to map the pet into the anatomical space

On 06/28/2016 01:48 PM, Pradeep wrote:
> Hello All,
>
> I am trying to extract the SUV values a PET image
>
> mri_segstats --seg wmparc.mgz --sum petsuv.segstats.dat --i rPET 
> --ctab-default
>
> since rPET is supposed to be coregistered to MRI, I did the following
>
> mri_coreg --s MRI --mov PET --lta mri_coreg.lta
>
> which did not generate the coregistered image but just transformation.
>
> Is there a way to generate this image or to just input the 
> mri_coreg.lta as a flag to mri_segstats?
>
> Thanks,
> Pradeep
>
>
>
>
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Re: [Freesurfer] Unsupported slice timing pattern 5 in version 5.3.0

[Douglas N Greve]

try this version and let me know if it works.
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_convert
If not, please send me the dicom via filedrop below

On 06/30/2016 05:45 AM, Leonardo Tozzi wrote:
>
> To Whom it may concern,
>
>
> I have tried to run the recon-all pipeline on some T1 data and have 
> encountered the following error:
>
>
> nifti1Read(): unsupported slice timing pattern 5
>
>
> I have browsed the previous threads about it and it appears that it 
> should have been fixed in version 5.3 but that is the version I run 
> and the error is still there.
>
> The data has been converted to NIFTI from DICOM using MRIcron and I 
> don't have access to the original DICOMs.
>
> I have seen that someone posted a modified version of nifti1Read() in 
> the past and I was wondering if it was still available.
>
> I am running Freesurfer 5.3.0 on MacOSX El Capitan 10.11.3.
>
> Would you have any suggestions on how to proceed?
>
> Thank you very much.
>
> Yours faithfully,
>
>
>
> Leonardo Tozzi, MD
>
> PhD Student
>
> Trinity College Institute of Neuroscience
>
> College Green, Dublin 2
>
> Ireland
>
>
>
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Re: [Freesurfer] mris_preproc subject-volume mismatch

[Raney, Talia L.]

mris_preproc --target fsaverage --hemi lh --iv 
WADG77j/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz 
WADG77j/restingstate/bb.register.lta --iv 
WADG77k/restingstate/fc.lh-entorhinal.space.lh/lh-entorhinal/ces.nii.gz 
WADG77k/restingstate/bb.register.lta --projfrac 0.5 --out lh.ces.mgh
ERROR: number of input volumes (2) does not equal number of subjects (8)
It apparently thinks one volume is 4 subjects but when checking 
bb.register.lta, it doesn't appear to be the case.
Thanks!
Talia

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve 
[gr...@nmr.mgh.harvard.edu]
Sent: Wednesday, July 06, 2016 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mris_preproc subject-volume mismatch

can you send the terminal output?

On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
> Hi FreeSurfer users,
> I'm trying to use mri-preproc to do a group fMRI analysis(based on the 
> tutorial). However, I keep getting an error that the number of input volumes 
> does not equal number of subjects. It seems one volume is counted as 4 
> subjects. I'm wondering what the command determines to be the subject list 
> when you use the --iv flag.
> For reference, I'm basing it off of this command:
> mris_preproc --target fsaverage --hemi lh \
>--iv  fbirn-101/ces.nii fbirn-101/bb.register.lta \
>--iv  fbirn-103/ces.nii fbirn-103/bb.register.lta \
>--iv  fbirn-104/ces.nii fbirn-104/bb.register.lta \
>--iv  fbirn-105/ces.nii fbirn-105/bb.register.lta \
>--iv  fbirn-106/ces.nii fbirn-106/bb.register.lta \
>--projfrac 0.5 \
>--out lh.ces.mgh
> Thanks!
> Talia
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>
>

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Re: [Freesurfer] Not able to find file in gtmseg

[Douglas N Greve]

The subject name is the FreeSurfer subject name assigned when you ran 
recon-all to analyze the T1 anatomical MRI images. BTW, you need 
everything in native space to run the pipeline.
doug

On 06/30/2016 12:25 AM, Lee Subin Kristine wrote:
> Dear FreeSurfer experts,
>
> Hello,
> I am trying to use Freesurfer's (developmental version) PVE correction 
> tool and I haveone question.
>
> The data to be PVE-corrected are some preprocessed PET data downloaded 
> from the Alzheimer's DIsease Neuroimaging Initiative (ADNI) database. 
> Basiclly, the dynamic PET images have been co-registered to one 
> another, averaged, and spatially normalized to a common space. Now I 
> am trying to apply PVE-correction.
> It seems from your answers here 
> (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg43435.html) 
> that
>  
> you run the following commands:
> (1) gtmseg
> (2) bbregister
> (3) mri_gtmpvc
> (4) mri_glmfit
>
> When I enter gtmseg --s subject such as below ('Desktop/forFSsubin_2' 
> is location of the subject MRI and '019_S_4835_N3m_cub_ACPC.nii' is 
> the filename)
>
> /~/Desktop/forFSsubin_2$ gtmseg --s 019_S_4835_N3m_cub_ACPC.nii/
>
> I get: /
>
> ERROR: cannot find //019_S_4835_N3m_cub_ACPC.nii/
>
> I have changed directory to the folder where the subject MRI file is, 
> and I have typed the subject's filename correctly, but it keeps saying 
> the subject file cannot be found. Any ideas on what is wrong here?
>
> Any help would be appreciated.
> Thank you in advance.
>
> Regards,
> Subin
>
>
>
>
>
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MGH-NMR Center
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Re: [Freesurfer] registering to fsaverage

[Douglas N Greve]

Trisanna, has this issue been resolved?
doug

On 06/30/2016 01:26 PM, Trisanna Sprung-Much wrote:
> Hi Bruce
>
> here is the output of my mri_vol2surf for a volumetric spam created in 
> minc tools. When I then overlay this result in Freeview, it displays a 
> Min of 127 and a Max of 255.
>
> trisanna@kaplan:~$ mri_vol2surf --mov 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc
>  
> --o 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
>  
> --hemi lh --surf pial --regheader MNI_average_2009a_asymm
> srcvol = 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_minc1.mnc
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = pial
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> INFO: changing type to float
> Done loading volume
> Computing registration from header.
>   Using 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/mri/orig.mgz as 
> target reference.
> Reading surface 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/surf/lh.pial
> Done reading source surface
> Mapping Source Volume onto Source Subject Surface
>  1 0 0 0
> using old
> Done mapping volume to surface
> Number of source voxels hit = 95521
> Writing to 
> /data-01/trisanna/freesurfer/MNI_average_2009a_asymm/spam_for_label_id_4_blur_overlay.mgz
> Dim: 152257 1 1
>
>
> --
> Ph.D. Candidate
> McGill University
> Integrated Program in Neuroscience
> Psychology
>
>
> On Wed, Jun 29, 2016 at 8:10 PM, Bruce Fischl 
> > wrote:
>
> Can you send the full output of that command?
>
> On Jun 29, 2016, at 2:54 PM, Trisanna Sprung-Much
>  > wrote:
>
>> Hi Bruce
>>
>> I simply use
>>
>> mri_vol2surf --mov spam.mnc --output overlayspam.mgz --regheader
>> subject --hemi lh --surf pial
>>
>> Trisanna
>>
>> --
>> Ph.D. Candidate
>> McGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 29, 2016 at 1:23 PM, Bruce Fischl
>> >
>> wrote:
>>
>> how do you create the overlay?
>> On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> Hi Bruce
>>
>> To create the spam I used minctools:
>>
>>  mincaverage  input.mnc output.mnc
>>
>> I blurred the spam using
>>
>> mincblur input.mnc output.mnc -fwhm 3
>>
>> When I open the spams using minc software, the % shown is
>> from about 10-40%
>> (i.e. the max overlap). For some reason when I create an
>> overlay from this
>> it displays the % from 1-255.
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Wed, Jun 29, 2016 at 12:20 PM, Bruce Fischl
>> > >
>> wrote:
>>   Hi Trisanna
>>
>>   what commands did you use to generate the
>> volumetric probability
>>   map?
>>
>>   Bruce
>>
>>
>>
>>   On Wed, 29 Jun 2016, Trisanna Sprung-Much wrote:
>>
>> Hi Bruce
>> So, when I take a probability map formed using
>> linear volumetric
>> registration with minc tools and saved as
>> .mnc and
>> convert it to an
>> overlay.mgz and open it in Freeview, the
>> probability
>> seems to be out of 255
>> (See the image attached). This is different
>> from my
>> Freesurfer generated
>> probability maps where I use -p in the
>> mri_average
>> command.
>>
>> Is there a way to change these probability values
>> that are displaying from
>> 1-255?
>>
>> many thanks
>>
>> Trisanna
>>
>> --
>> Ph.D. CandidateMcGill University
>> Integrated Program in Neuroscience
>> Psychology
>>
>>
>> On Mon, Jun 27, 2016 at 10:28 AM, Bruce Fischl
>> > >
>> wrote:
>>   Hi Trisanna
>>
>>   

Re: [Freesurfer] convert from MNI152 to native space

[Douglas N Greve]

Is this problem resolved? There is a new version here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mni152reg

On 06/16/2016 11:05 AM, Leila Reddy wrote:
> Hi FS Experts,
>
> I'm trying to use the mni152reg command but I get an error that --lta 
> is not recognized.
>
> It appears that fslregister doesn't have this option. There was a 
> previous post about this problem
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg41953.html
>
> but I can't figure out if the problem had been solved. The version of 
> mni152reg I am using is
> $Id: mni152reg,v 1.9 2014/07/07 18:59:08 greve Exp $ on Mac OS 10.8.
>
>
> Thanks,
> Leila
>
>
> On Wednesday, June 15, 2016 11:55 AM, Leila Reddy  wrote:
>
>
> Hi,
>
> I have a binary mask from the WFU_Pickatlas. I think this mask in in 
> the MNI152 space (when I load_nifti in Matlab I get dimensions of [91 
> 109 91]. I would like to convert this mask into the native space of 
> each subject. I tried the following command but the results do not 
> look right in Freeview:
>
>  mri_vol2vol --mov mask_MNI152.nii --targ bold/005/f.nii.gz --o 
> mask_in_Native.nii --mni152reg
>
> The overlay of the mask on f.nii in Freeview is mostly outside the brain.
>
> How can I go about this step?
>
> Thanks for your help,
> Leila
>
>
>
>
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Re: [Freesurfer] Intensity stats question

[Douglas N Greve]

On 07/06/2016 01:05 PM, Sabrina Yu wrote:
>
> Hello,
>
>
> I have a couple of questions about the wmparc.stats file generated. 
> What volume is the data based on?
>
norm.mgz
>
> Has the intensity of the volume been corrected?
>
Yes
>
> I just need the average voxel intensity over the ROIs, but am unsure 
> if this intensity is based on an intensity normalized brain volume.
>
>
> Is it possible to change the input volume for wmparc.stats to orig.mgz?
>
Look in the subject/scripts/recon-all.log file for the mri_segstats 
command that generates the wmparc.stats file
>
>
> Thank you in advance.
>
>
>
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Re: [Freesurfer] mris_preproc subject-volume mismatch

[Douglas N Greve]

can you send the terminal output?

On 07/06/2016 11:32 AM, Raney, Talia L. wrote:
> Hi FreeSurfer users,
> I'm trying to use mri-preproc to do a group fMRI analysis(based on the 
> tutorial). However, I keep getting an error that the number of input volumes 
> does not equal number of subjects. It seems one volume is counted as 4 
> subjects. I'm wondering what the command determines to be the subject list 
> when you use the --iv flag.
> For reference, I'm basing it off of this command:
> mris_preproc --target fsaverage --hemi lh \
>--iv  fbirn-101/ces.nii fbirn-101/bb.register.lta \
>--iv  fbirn-103/ces.nii fbirn-103/bb.register.lta \
>--iv  fbirn-104/ces.nii fbirn-104/bb.register.lta \
>--iv  fbirn-105/ces.nii fbirn-105/bb.register.lta \
>--iv  fbirn-106/ces.nii fbirn-106/bb.register.lta \
>--projfrac 0.5 \
>--out lh.ces.mgh
> Thanks!
> Talia
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>
>

-- 
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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] question about white matter edits

[Barbara Kreilkamp]

Hi Rito,

I just read this today myself "Select a few control points around your 
trouble areas, space them out throughout the brain and on different 
slices. You want to pick points in a region where the wm intensity is 
lower than it should be (that is, having a voxel value less than 110)." 
from 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints_freeview


Could it be that those control points grasp voxels that already have an 
intensity of at least 110?


Best wishes,

Barbara




On 06/07/2016 17:25, Ritobrato Datta wrote:

Hi All,

We have run recon-all on T1 FLASH images have identified regions where the 
sulci were included inside the white matter boundary. We added controls points 
around the sulci (please see attached pic) and reran recon-all as follows

recon-all -autorecon2-cp -autorecon3 -subjid 

but on a lot of instances, the specified control points were not incorporated 
(please see attached image). How do we fix this, now that we have already run 
the recon-all with -autorecon2-cp and the error persists ?

Can someone please suggest ?

Thank you,

Rito and Jack



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[Freesurfer] Intensity stats question

[Sabrina Yu]

Hello,


I have a couple of questions about the wmparc.stats file generated. What volume 
is the data based on? Has the intensity of the volume been corrected? I just 
need the average voxel intensity over the ROIs, but am unsure if this intensity 
is based on an intensity normalized brain volume.


Is it possible to change the input volume for wmparc.stats to orig.mgz?


Thank you in advance.
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[Freesurfer] TRACULA tract group comparison p-values

[Barbara Kreilkamp]

Dear Freesurfers,

I am looking for a way to add a colorbar to my p-value tract cores 
generated through TRACULA.

When I load up the images as described in the tutorial here 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics

I only get a colorbar from 0 to 28.5 which cannot reflect pvalues, and 
there is no option to select my textfile with the p-values unfortunately.

Would you please help?

Thanks ever so,

Barbara

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[Freesurfer] mris_preproc subject-volume mismatch

[Raney, Talia L.]

Hi FreeSurfer users,
I'm trying to use mri-preproc to do a group fMRI analysis(based on the 
tutorial). However, I keep getting an error that the number of input volumes 
does not equal number of subjects. It seems one volume is counted as 4 
subjects. I'm wondering what the command determines to be the subject list when 
you use the --iv flag.
For reference, I'm basing it off of this command:
mris_preproc --target fsaverage --hemi lh \
  --iv  fbirn-101/ces.nii fbirn-101/bb.register.lta \
  --iv  fbirn-103/ces.nii fbirn-103/bb.register.lta \
  --iv  fbirn-104/ces.nii fbirn-104/bb.register.lta \
  --iv  fbirn-105/ces.nii fbirn-105/bb.register.lta \
  --iv  fbirn-106/ces.nii fbirn-106/bb.register.lta \
  --projfrac 0.5 \
  --out lh.ces.mgh
Thanks!
Talia
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Re: [Freesurfer] hippocampal subfields command

[Alexopoulos, Dimitrios]

Thanks. Only for FS 6.0 and later, correct?

Jim

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias, Eugenio
Sent: Wednesday, July 06, 2016 9:47 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] hippocampal subfields command

Hi Jim,
the latter command uses a new, higher resolution atlas based on ex vivo scans.
Cheers,
Eugenio

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

On 6 Jul 2016, at 15:39, Alexopoulos, Dimitrios 
> wrote:

A quick question re: hippocampal segmentation.

I have processed 1mm isotropic T1 data with 5.3 using the following command:
recon-all  -qcache -all  -hippo-subfields

How is this this different than using the following command I have found here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
-hippocampal-subfields-T1


Thanks.
Jim


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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Iglesias, Eugenio]

Not yet, sorry. But it’s on my todo list.


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


On 6 Jul 2016, at 14:39, Hibert, Matthew Louis 
> wrote:

Hi Eugenio,
Have you had a chance to look into the possibility of combining the -hires flag 
with the hippocampal subfield segmentation?

Thanks,
Matt

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk]
Sent: Friday, June 10, 2016 3:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Matt,
Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t 
crash when you run it! That said, I need to go through the code, and make sure 
that data are handled the way they are supposed to: the fact that it doesn’t 
crash doesn’t directly imply that it is working properly. Hopefully I’ll find 
time to do this next week…
Cheers,
Eugenio


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


On 9 Jun 2016, at 21:51, Hibert, Matthew Louis 
> wrote:

Hi Eugenio,
Would it also be possible to use the -hires flag in the initial recon-all 
command to prevent the T1 from being downsampled and maintain the voxel size 
that the T1 was acquired at, and use that resulting recon for the hippocampal 
subfield segmentation?  I've tested this with MEMPRAGE scans acquired at 0.75mm 
isotropic and coronal T2 anisotropic scans acquired at 0.33mm in plane with 1mm 
thick slices, and the results look reasonable.  The "1mm" label files are 
correctly downsampled to 0.75mm instead of 1mm, and the higher resolution label 
files remain at 0.33mm resolution.

Thanks,
Matt

Stufflebeam Lab
Athinoula A. Martinos Center
Massachusetts General Hospital
149 13th Street, Room 1115S
Charlestown, MA 02129

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

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


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to 

Re: [Freesurfer] hippocampal subfields command

[Iglesias, Eugenio]

Hi Jim,
the latter command uses a new, higher resolution atlas based on ex vivo scans.
Cheers,
Eugenio

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


On 6 Jul 2016, at 15:39, Alexopoulos, Dimitrios 
> wrote:

A quick question re: hippocampal segmentation.

I have processed 1mm isotropic T1 data with 5.3 using the following command:
recon-all  -qcache -all  -hippo-subfields

How is this this different than using the following command I have found here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
-hippocampal-subfields-T1


Thanks.
Jim


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[Freesurfer] hippocampal subfields command

[Alexopoulos, Dimitrios]

A quick question re: hippocampal segmentation.

I have processed 1mm isotropic T1 data with 5.3 using the following command:
recon-all  -qcache -all  -hippo-subfields

How is this this different than using the following command I have found here: 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields
-hippocampal-subfields-T1


Thanks.
Jim


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Re: [Freesurfer] segmentation issues in Temporal Lobes

[Barbara Kreilkamp]

Dear Bruce,

Thanks a lot for clarifying.

Best wishes,

Barbara


On 06/07/2016 15:57, Bruce Fischl wrote:
> Hi Barbara
>
> yes, this is intentional and shouldn't be a problem. The hippocampus has
> lots of internal structure that we don't model with the surfaces (but we do
> with the subfield stuff), but we exclude it from our analyses so you should
> be fine
>
> cheers
> Bruce
>
> On Wed, 6 Jul 2016, Barbara Kreilkamp
> wrote:
>
>> Dear Freesurfers,
>>
>> Unfortunately I am having a problem with recon-all segmentation in some of my
>> participants.
>>
>> It seems that part of the brain is cut off in the medial part of the Temporal
>> lobes (please see attachment), around the region where the hippocampus is.
>>
>> I am unable to place WM region control points, as the algorithm does not have
>> seemed to miss white matter, rather only gray matter of the hippocampus.
>>
>> I've seen on your website that also there the cortical surface does not
>> include the hippocampus, so I wonder if this is intentional? Problem is that
>> the surface here grasps some of the hippocampus but not all of it.
>>
>> What is the best way of solving this?
>>
>> Thanks very much.
>>
>> Best wishes,
>>
>> Barbara
>>
>>
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Re: [Freesurfer] Inquiries about the curvature

[Bruce Fischl]

Hi Mahtab

you should look them up in a differential geometry textbook. Essentially, 
a 2D surface has two curvatures at each point, one in the direction of 
maximum folding (k1) and one in the direction of minimum folding (k2). The 
Gaussian curvature is then k1*k2 and the mean is (k1+k2)/2


cheers
Bruce

On 
Wed, 6 Jul 2016, Mahtab Farahbakhsh wrote:



Dear FreeSurfer,
I am using the mris_anatomical_stats output to calculate the curvature and
thickness indices for different brain areas. However, I am not sure what the 
mean
and gaussian curvatures mean. I could not find a complete description on these
two. Would you please guide me what principle curvature and mean and gaussian
curvatures means exactly?

I appreciate your concern in advance.

Best Regards,
Mahtab. 

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Re: [Freesurfer] FSFAST time series extraction

[Sabin Khadka]

Hi Doug,

Yes. Dr. Yeo Thomas helped me figuring out ways to extract ROI values from
Buckner 2011 7 Cerebellar network. Please see below for the steps I
performed to extract time series from Buckner 2011 7 Cerebellar networks.
If you could give your thoughts on the steps/process that'd be great.

*1. Run MNI152 1mm template through recon-all*
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid
Yeo2011_MNI152_FS
recon-all -all Yeo2011_MNI152_FS

*2. Warp the Buckner_atlas1mm.nii.gz (use the LooseMask) to
freesurfe nonlinear volumetric space*
mri_vol2vol --mov
$FREESURFER_HOME/average/Buckner_JNeurophysiol11_MNI152/Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
\
--s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z
talairach.m3z --o BucknerAtlas1mm_FSL.nii.gz --nearest

*3. warp the BucknerAtlas1mm_FSI.nii.gz from freesurfer nonlinear*
volumetric space to each subject:
mri_vol2vol --mov $SUBJECTS_DIR/FSSub/mri/norm.mgz --s FSSub --targ
BucknerAtlas1mm_FSL.nii.gz --m3z talairach.m3z --o
Buckner2011_atlas_FSSub.nii.gz --nearest --inv-morph


*4. Create a cerebellum gray matter mask in the native subject's space by
applying mri_binarize to aparc2009s+aseg.mgz of the subject*

mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 8  --o
cerebellum_mask_FSSub_m8.nii.gz #  For left
mri_binarize --i FSSub/mri/aparc.a2009s+aseg.mgz --match 47 --o
cerebellum_mask_FSSub_m47.nii.gz #  FOr right


*5. Using this mask to mask the Buckner cerebellum parcellations*

fslmaths Buckner2011_atlas_FSSub.nii.gz -mas
cerebellum_mask_FSSub_m8.nii.gz Buckner_atlas_FSSub_m8.nii.gz #  For
left
fslmaths Buckner2011_atlas_FSSub.nii.gz -mas
cerebellum_mask_FSSub_m47.nii.gz Buckner_atlas_FSSub_m47.nii.gz #  For
right

*6. Functional data to anatomical space*

mri_vol2vol --mov fmcpr.nii.gz --fstarg --reg register.dof6.dat --o
fmcpr.anat.nii.gz #  functional into anatomical space

*7. Extract L/R Cerebellar ROIs time series*

 mri_segstats --seg
{analysisrootdir}/analysis/Buckner_atlas_FSSub_m8.nii.gz   --ctab
$FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt
--excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_L.txt #
 extract Left Cerebellum time series
mri_segstats --seg
{analysisrootdir}/analysis/Buckner_atlas_FSSub_m47.nii.gz  --ctab
$FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/Yeo2011_7Networks_ColorLUT.txt
--excludeid 0 --i fmcpr.anat.nii.gz --avgwf Cerebellum_networks_R.txt #
 extract right Cerebellum time series

Cheers,
Sabin Khadka

On Tue, Jul 5, 2016 at 3:48 PM, Douglas N Greve 
wrote:

> has this question been answered?
>
> On 06/17/2016 09:42 AM, curry_sa...@yahoo.com wrote:
> > Hi all,
> >
> > I am trying to extract mean time series BOLD data using FSFAST from
> > Cortical ROIs + sub cortical ROIs and cerebellum.
> >
> > preproc-sess -s rest210 -fsd bold -surface fsaverage lhrh -mni305
> > -fwhm 6 -per-run -stc oddmri_segstats --annot fsaverage lh aparc
> > --i rest210/bold/001/fmcpr.odd.sm6.fsaverage.lh.nii.gz --excludeid
> > 1000 --excludeid 1004 --avgwf CorticalTimeSeries_lh.txt
> > mri_segstats --annot fsaverage rh aparc --i
> > rest210/bold/001/fmcpr.odd.sm6.fsaverage.rh.nii.gz --excludeid 2000
> > --excludeid 2004 --avgwf CorticalTimeSeries_rh.txt
> >
> > and for cortical time series
> >
> > mri_segstats --seg fsaverage/mri.2mm/aseg.mgz --ctab
> > /opt/freesurfer/FreeSurferColorLUT.txt --id 10 --id 11 --id 12 --id 13
> > --id 17 --id 18 --id 26 --id 49 --id 50 --id 51 --id 52 --id 53 --id
> > 54 --id 58 --i rest210/bold/001/fmcpr.odd.sm6.mni305.2mm.nii.gz
> > --avgwf subCorticalTimeSeries.txt
> >
> > But I am not sure on how exactly to extract time series from
> > cerebellar regions. So if I want to extract time series from regions
> > as described in Buckner et.al 2011. Could I just use mri_segstats for
> > the labels 601-628 in FreeSurferCololLUT.txt? If not could you please
> > direct me to processes that I can use.
> >
> >
> >
> > Sent from Yahoo Mail. Get the ap 
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
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>
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> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you 

Re: [Freesurfer] segmentation issues in Temporal Lobes

[Bruce Fischl]

Hi Barbara

yes, this is intentional and shouldn't be a problem. The hippocampus has 
lots of internal structure that we don't model with the surfaces (but we do 
with the subfield stuff), but we exclude it from our analyses so you should 
be fine

cheers
Bruce

On Wed, 6 Jul 2016, Barbara Kreilkamp 
wrote:

> Dear Freesurfers,
>
> Unfortunately I am having a problem with recon-all segmentation in some of my 
> participants.
>
> It seems that part of the brain is cut off in the medial part of the Temporal 
> lobes (please see attachment), around the region where the hippocampus is.
>
> I am unable to place WM region control points, as the algorithm does not have 
> seemed to miss white matter, rather only gray matter of the hippocampus.
>
> I've seen on your website that also there the cortical surface does not 
> include the hippocampus, so I wonder if this is intentional? Problem is that 
> the surface here grasps some of the hippocampus but not all of it.
>
> What is the best way of solving this?
>
> Thanks very much.
>
> Best wishes,
>
> Barbara
>
>
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Re: [Freesurfer] Freesurfer/Freeview help

[Bruce Fischl]

Hi Abbie

you might check out Matti Hamalainen's MNE software. He does both boundary 
and finite element analysis. We distribute a test subject named "bert" you 
can use


cheers
Bruce
 On Tue, 5 Jul 2016, Abbie McNulty wrote:


Hello,
Just a couple more questions that would be great if you could answer in
explanation form:

How do people develop finite element models from brain MRI?
How do people learn and implement the software on an example data set?

Abbie

On Tue, Jul 5, 2016 at 9:42 AM, Abbie McNulty  wrote:
  Hello,
Just a couple more questions that would be great if you could answer in
explanation form:

How do people develop finite element models from brain MRI?
How do people learn and implement the software on an example data set?

Abbie 

On Mon, Jun 27, 2016 at 6:37 PM, Bruce Fischl 
wrote:
  Hi Abbie

  you just use the recon-all script from the command line:

  recon-all \
          -i  \
          -sd  \
          -s  \
          -all

  this will take 5-20 hours and at the end will create and
  populate a
  directory tree with segmented volumes and surfaces
  cheers
  Bruce

          On Mon, 27 Jun
  2016, Abbie McNulty wrote:

  > Hi Bruce,
  > I am trying to create a mesh of the MRI scans, eventually
  with imported
  > scans, but for now just using the information available
  through the
  > software. How do you work these voxel segmentations? I'm just
  very new with
  > the software.
  >
  > Say I import an MRI scan, and I want to cortically segment it
  in order to
  > create a mesh of the volume. What are the steps to do this
  and how do I
  > follow through with each step? I tried to watch the youtube
  tutorials on the
  > Freesurfer youtube, but since they are slides informing of
  what Freesurfer
  > can do and not quite a play-by-play interaction of Freeview,
  I am stuck.
  >
  > Thanks
  >
  > Abbie
  >
  > On Mon, Jun 27, 2016 at 3:30 PM, Bruce Fischl
  
  > wrote:
  >       Hi Abbie
  >
  >       what are you trying to create a mesh of? We supply
  meshes for
  >       the
  >       gray/white interface and for the pial surface. We
  supply voxel
  >       segmentations of lots of other things that you could
  mesh, but
  >       we don't
  >       by default.
  >
  >       cheers
  >       Bruce
  >       On Mon, 27 Jun 2016, Abbie McNulty wrote:
  >
  >       > Hello,
  >       > I am trying to segment a MRI brain in order to create
  a mesh
  >       of the image
  >       > into finite elements, but I am very new with
  >       Freesurfer/Freeview and am not
  >       > familiar with the tools. So far, I have only uploaded
  >       brain.mgt from the
  >       > bert file that comes with the program. If I wanted to
  mesh
  >       this brain, how
  >       > should I proceed? The online tutorials have confused
  me
  >       especially since I
  >       > am not sure if I am supposed to be using the terminal
  or the
  >       command window
  >       > for a lot of the code commands.
  >       >
  >       > Any help would be appreciated.
  >       >
  >       > Thanks!
  >       >
  >       > Abbie McNulty
  >       >
  >       > --
  >       > Abigail C. McNulty
  >       > Stanford University Class of 2018
  >       > B.A. Candidate in Bioengineering
  >       > Stanford Women's XC/ Track and Field
  >       >
  >       >
  > ___
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  > The information in this e-mail is intended only for the
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  > it is
  > addressed. If you believe this e-mail was sent to you in
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  > in error
  > but does not contain patient information, please contact the
  sender
  > and properly
  > dispose of the e-mail.
  >
  >
  >
  >
  > --
  > Abigail C. McNulty
  > Stanford University Class of 2018
  > B.A. Candidate in Bioengineering
  > Stanford Women's XC/ Track and Field
  >
  >
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--
Abigail C. McNulty
Stanford University Class of 2018
B.A. Candidate in 

Re: [Freesurfer] Fwd: Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?

[Douglas Greve]

See if this page helps

http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats


On 7/6/16 9:07 AM, Kaiming Yin wrote:

Dear experts,

Could I ask which value in the stats/aseg.stats represents the volume 
of the cerebrum (including the subcortical structures while excluding 
the ventricles and brain stem)? I'm not sure whether the 
"SupraTentorialNotVent" can be the value for this measurement, and 
could it be a bit bigger than the real value due to the partial volume 
effect?


Besides, could I also ask is there a value represent the volume of the 
cerebellum? Currently I calculate the volume by adding the left/right 
cerebellar GM/WM values in the detailed list in aseg.stats file.


Many thanks,
Kaiming



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Re: [Freesurfer] segmentation issues in Temporal Lobes

[Harms, Michael]

Hi,
There is nothing to solve — that is the expected behavior around the
hippocampus/amygdala.

See this FAQ:
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurfac
esnearthemedialwall.2Chippocampus.2Candamygdalaaren.27taccuratelyfollowingt
hestructuresthere.HowcanIfixthis.3F

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 7/6/16, 4:47 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Barbara Kreilkamp"  wrote:

Dear Freesurfers,

Unfortunately I am having a problem with recon-all segmentation in some
of my participants.

It seems that part of the brain is cut off in the medial part of the
Temporal lobes (please see attachment), around the region where the
hippocampus is.

I am unable to place WM region control points, as the algorithm does not
have seemed to miss white matter, rather only gray matter of the
hippocampus.

I've seen on your website that also there the cortical surface does not
include the hippocampus, so I wonder if this is intentional? Problem is
that the surface here grasps some of the hippocampus but not all of it.

What is the best way of solving this?

Thanks very much.

Best wishes,

Barbara




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Re: [Freesurfer] mri_surfcluster

[Douglas Greve]

use this program

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



On 7/6/16 9:22 AM, tom parker wrote:

Dear Freesurfers,

I ran a comparison between different groups using mri_glmfit.
Now I would like to correct the results in sig.mgh by multiple 
comparisons using FDR. I tried using tksurfer but it doesn't work so 
well on my computer and I read that freeview does not allow to do that 
yet.


I'm now trying to use mri_surfcluster to do it. Is this correct?
mri_surfcluster --in sig.mgh --subject fsaverage --surf inflated 
--hemi lh --fdr 0.05 --sign pos


After I run it some thresholds appear in the terminal.
Should I use these thresholds to create a FDR corrected sig.mgh map or 
is there a direct way of getting this using mri_surfcluster or other 
command?


Thank you so much!



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Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[Hibert, Matthew Louis]

Hi Eugenio,
Have you had a chance to look into the possibility of combining the -hires flag 
with the hippocampal subfield segmentation?

Thanks,
Matt

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk]
Sent: Friday, June 10, 2016 3:36 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Matt,
Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t 
crash when you run it! That said, I need to go through the code, and make sure 
that data are handled the way they are supposed to: the fact that it doesn’t 
crash doesn’t directly imply that it is working properly. Hopefully I’ll find 
time to do this next week…
Cheers,
Eugenio


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


On 9 Jun 2016, at 21:51, Hibert, Matthew Louis 
> wrote:

Hi Eugenio,
Would it also be possible to use the -hires flag in the initial recon-all 
command to prevent the T1 from being downsampled and maintain the voxel size 
that the T1 was acquired at, and use that resulting recon for the hippocampal 
subfield segmentation?  I've tested this with MEMPRAGE scans acquired at 0.75mm 
isotropic and coronal T2 anisotropic scans acquired at 0.33mm in plane with 1mm 
thick slices, and the results look reasonable.  The "1mm" label files are 
correctly downsampled to 0.75mm instead of 1mm, and the higher resolution label 
files remain at 0.33mm resolution.

Thanks,
Matt

Stufflebeam Lab
Athinoula A. Martinos Center
Massachusetts General Hospital
149 13th Street, Room 1115S
Charlestown, MA 02129

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Iglesias, Eugenio 
[e.igles...@ucl.ac.uk]
Sent: Thursday, June 09, 2016 2:36 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the 
voxel size of the input?

Hi Fernando,

Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code 
assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to 
take advantage of multiple images with higher resolution, but it hasn’t been 
thoroughly tested and it’s not publicly available at this point.
That said, there are different things you can do at this point:
1. Use the T1+T2 as is (disadvantage: T1 will be resampled to 1 mm).
2. Use only the T2.
3. Use only the T1. To do this, you would use the T1 as additional scan on its 
own (i.e., the main and additional scans are the same, but the additional one 
won’t be resampled).
4. There might be a way (hack) of using both scans at full resolution. If you 
change the header of the T1 scan and specify that the voxel size is 1mm, no 
resampling will happen; FreeSurfer will believe that you’re dealing with a 
subject with a very large head. If you do this, you’ll also have to enlarge the 
voxel size of the T2 by a factor 1/0.7. Also, the resulting volumes will have 
to be divided by (1/0.7)^3 in order to correct for the “wrong” voxel size.

I hope this helps!

Cheers,

Eugenio

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


On 9 Jun 2016, at 19:23, Fernando Pasquini Santos 
> wrote:

Dear,

I have a doubt regarding the input T1 image used for the Hippocampal Subfield 
segmentation in Freesurfer 6.0 - 
https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfields

In this documentation it says that I can use a standard 1mm T1 image or the 
same standard 1mm T1 image with an additional scan. However, I want to use a 
0.7mm T1 image as input, with an additional T2 scan. When I run the program 
with it, the output images (nu.mgz and orig.mgz) are downsampled to 1mm voxel 
size. So, I don't know if this happens just because of the recon-all program or 
if the segmentation is being done in the downsampled T1 image or in the 
original 0.7mm.

By reading the article "A computational atlas of the hippocampal formation 
using ex vivo, ultra-high resolution MRI: Application to adaptive segmentation 
of in vivo MRI" I saw that, in the methods section, the algorithm is used to 
segment 0.6mm T1 images. But is this possible to do in the Freesurfer package? 
Obviously, doing the segmentation directly on 0.7mm data would be better than a 
downsampled version to 1mm...

Thanks,

Fernando Pasquini Santos
PhD student in Dynamic Systems
fernandosan...@pitt.edu

[Freesurfer] mri_surfcluster

[tom parker]

Dear Freesurfers,

I ran a comparison between different groups using mri_glmfit.
Now I would like to correct the results in sig.mgh by multiple comparisons
using FDR. I tried using tksurfer but it doesn't work so well on my
computer and I read that freeview does not allow to do that yet.

I'm now trying to use mri_surfcluster to do it. Is this correct?
mri_surfcluster --in sig.mgh --subject fsaverage --surf inflated --hemi lh
--fdr 0.05 --sign pos

After I run it some thresholds appear in the terminal.
Should I use these thresholds to create a FDR corrected sig.mgh map or is
there a direct way of getting this using mri_surfcluster or other command?

Thank you so much!
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[Freesurfer] Fwd: Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?

[Kaiming Yin]

Dear experts,

Could I ask which value in the stats/aseg.stats represents the volume of
the cerebrum (including the subcortical structures while excluding the
ventricles and brain stem)? I'm not sure whether the
"SupraTentorialNotVent" can be the value for this measurement, and could it
be a bit bigger than the real value due to the partial volume effect?

Besides, could I also ask is there a value represent the volume of the
cerebellum? Currently I calculate the volume by adding the left/right
cerebellar GM/WM values in the detailed list in aseg.stats file.

Many thanks,
Kaiming
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[Freesurfer] Inquiries about the curvature

[Mahtab Farahbakhsh]

Dear FreeSurfer,

I am using the mris_anatomical_stats output to calculate the curvature and
thickness indices for different brain areas. However, I am not sure what
the mean and gaussian curvatures mean. I could not find a complete
description on these two. Would you please guide me what principle
curvature and mean and gaussian curvatures means exactly?

I appreciate your concern in advance.

Best Regards,
Mahtab.
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Re: [Freesurfer] Hippocampal Subfields Segmentation

[Iglesias, Eugenio]

Dear all,

We are working on this; I'll write again when the problem is solved (hopefully 
soon!)

Cheers

Eugenio


Juan Eugenio Iglesias

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of pierre deman 

Sent: Tuesday, July 5, 2016 7:04:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation


Hi,
I still have a problem as well with the subfields segmentation (ubuntu 14.04, 
with the files .ctf)

Cheers,
Pierre

Hello FreeSurfer Experts,

I'm having issues with the hippocampal subfields segmentation using OS X 
Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer  Subject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0   Current Stamp: 
freesurfer-Linux-centos6_x86_64-dev-20160616-8264611.

I ran the recon-all -s VE002 -hippocampal-subfields-T1 command and keep getting 
an error message : Error:CTF file 
'/usr/local/freesurfer-dev/bin/segmentSubjectT1_autoEstimateAlveusML.ctf' 
failed to open for 'Read' access. Error message: 'Open a zip file for 
read/modify failed.'

The segmented hippocampal files as described on free surfer wiki cannot be 
found under the subject 'mri' folder.
I understand other users have complained of a similar issue within the last 
week.

I'd ve grateful if you could assist me with the issue above.

Many thanks
Permesh




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