[Freesurfer] hippocampal-subfields segmentation failure

[Xiaofu]

External Email - Use Caution

Hello,

   I am running segmentation of hippocampal subfields in FreeSurfer 6.0 but
one subject failed running the segmentation with the following error
message.

Wrote image to file asmr2.mgz

This file does not contain MRI parameters

This file does not contain MRI parameters

In an assignment  A(:) = B, the number of elements in A and B must be the
same.

Error in segmentSubjectT1_autoEstimateAlveusML (line 1848)



Any suggestions on this?  Thank you very much!


Best,

Xiaofu
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Re: [Freesurfer] projfrac question

[Nasiriavanaki, Zahra]

I did not find mri_vol2surf.

Below is part of a log file, as you see  -projrfac has changed to 0.5 but not  
to 0.2.

mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg 
bold/020/tmp.bbregister.43919/reg.init.dat --out-reg 
bold/020/tmp.bbregister.43919/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 
--tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 
--gm-gt-wm 0.5
$Id: mri_segreg.c,v 1.113 2016/05/10 03:23:20 greve Exp $
setenv SUBJECTS_DIR /autofs/space/oprah_001/users/jvm27/looming/SUBJECTS_DIR
cd /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T
mri_segreg --mov bold/020/tmp.bbregister.43919/template.nii --init-reg 
bold/020/tmp.bbregister.43919/reg.init.dat --out-reg 
bold/020/tmp.bbregister.43919/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 
--tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 
--gm-gt-wm 0.5


Thanks

Mona






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

Sent: Thursday, February 28, 2019 2:54:51 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] projfrac question

I would have thought that it would have changed. Can you look through
the logs and find the mri_vol2surf command and verify that the
--projfrac argument is changing?

On 2/28/19 2:51 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> Thank you very much for your reply.
>
> I was actually using -force and It did take a reasonable amount of time.
>
> Then I ran the selxavg command to get the first level maps, and I
> guess It used the last preprocessd data which was from projfrac 0.2.
>
>
> Thanks
>
> Mona
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Thursday, February 28, 2019 2:41:25 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] projfrac question
> The projfrac function might not be working in the way that you think. It
> might not actually be re-running anything. Did preproc-sess finish
> faster than you would have expected? You can try deleting the projfrac
> output and re-running. You can also run preproc-sess with -force, but
> this will force it to re-run everything. If you want to use multiple
> project fracs, then you should copy the functional tree to a new
> location (if you use -p with cp, it will copy the modification time,
> which will make preproc-sess run faster).
>
> On 2/28/19 12:55 PM, Nasiriavanaki, Zahra wrote:
> >
> > Dear Freesurfers
> >
> >
> > Hi
> >
> > I was trying to look at the activation in different cortical layers in
> > a _single subject_.
> >
> > I ran my preproc-sess command three times, once without using
> > -projfrac flag, once  -projfrac 0.5 and lastly -projfrac 0.2
> >
> > The activation patterns are exactly the same.
> >
> > My voxel sizes are 1.1*1.1*1.1 .
> >
> > My question is:
> >
> > 1-Is it normal that the activations do not change at all the more I
> > get closer to white matter?
> >
> > 2-when I use -projfrac 0.2 , does it mean that I am averaging the
> > activation between white matter layer to 0.2 of gray matter layer? Or
> > is it averaging the activation between pial surface to 0.2 gray matter?
> >
> >
> > I hope my questions are clear.
> >
> >
> > Thanks
> >
> > Mona
> >
> >
> >
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To see the collection of prior postings to the list, visit the Freesurfer 
Archives.. A searchable archive which of messages PRIOR to March 2004 is at 
this site A searchable archive which includes messages AFTER March 2004 is at 
this site. Using Freesurfer



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Re: [Freesurfer] dt_recon --> tbss

[Daniel Callow]

External Email - Use Caution

I was also running an ROI analysis based on the recon-all segmentations so
I figured I could use the FA results and skip the process of running
through the whole tbss process. I also found dt_recon's ability to
determine bvals and bvecs from the dcm without needing to create the txt
files that fsl needed made the preprocessing steps simpler and less likely
to lead to human error in the process.
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Thu, Feb 28, 2019 at 3:05 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> no idea. If you want to use tbss, why not use FSL to do the dti analysis
> from the start?
>
> On 2/26/19 10:27 AM, Daniel Callow wrote:
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> > I am working through dt_recon troubleshooting  (One subjects
> > registration to anatomical is skewed leading to incorrect masking of
> > that subjects FA image). I would like to use the dt_recon's FA outputs
> > and input them into FSL's tbss pipeline. My question is are there any
> > steps I should take converting or modifying the FA images so they are
> > compatible with the tbss pipeline. My intention was to take the
> > dt_recon fa or fa-masked into the tbss_1_preproc command?
> >
> > Are there any considerations I should take into account?
> >
> > Best
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > _ddcc2...@gmail.com _
> > 443-254-6298
> >
> > ___
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>
>
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[Freesurfer] White Matter Edit

[Abazid, Leen]

External Email - Use Caution

Dear FreeSurfer supporter,


We are working on a PTSD project and we used FreeSurfer to obtain the 
subcortical and cortical volumes for our MRI images in our patients. We ran our 
images through the recon-all pipeline.   We then extracted the volumes from the 
lh/rh.aparc.stats files. We plotted the volume data for all the subjects for 
all the structures using SPSS to compare the volumes between the right and left 
hemispheres to identify outliers. After further inspection of our plots for the 
cingulate

structure, we believe the volumes are not accurate. The cingulate is very 
important in the pathogenesis of PTSD and we want to make sure the volumes we 
are getting are correct. We loaded the data into Freeview to check the gray and 
white matter segmentations and it appears that the white matter segmentation is 
including gray matter. We used the following command to edit the wm.mgz:


freeview -v mri/brainmask.mgz \
mri/wm.mgz:colormap=heat:opacity=0.4 \
-f surf/lh.white:edgecolor=blue \
surf/lh.pial:edgecolor=red \
surf/rh.white:edgecolor=blue \
surf/rh.pial:edgecolor=red \
surf/rh.inflated:visible=0 \
surf/lh.inflated:visible=0


After editing/cleaning we saved the new wm.mgz image and ran the following 
command:


recon-all -autorecon2-wm -autorecon3 -subjid#



Following completion we checked the new lh/rh.aparc.stats files? and the total 
white matter volume is increasing in some patients and decreasing in others 
while the gray matter is increasing in some of the subjects (which is what we 
expect). Do you have any suggestions for why the WM volumes would be increasing 
if we are removing what we think is not WM?  Are we running the correct 
commands to edit the WM segmentation?


Any suggestions or help would greatly appreciated.


Thanks,



Leen F. Abazid
Ph.D. Student
Neuroscience Imaging at the Research Imaging Institute
UT Health Science Center at San Antonio
(210) 823-3532

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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

[Greve, Douglas N.,Ph.D.]

Did you see the line "If you seek help with this problem, make sure to 
send:" and then it lists some things to send

On 2/25/19 2:13 PM, Arsenije Subotic wrote:
>
> External Email - Use Caution
>
> Dear experts,
>
> I have recently tried to use the command line to examine thickness 
> differences between two groups after controlling for the effects of 
> age and sex. I get the following error :
>
> ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
> 
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>   1. Your command line:
>     mri_glmfit.bin --y CAA_CTRL_RH.thickness.10.mgh --fsgd 
> CAA_CTRL_RH_Age_Sex.fsgd --C Contrasts/CAA-CTRL_Age_Sex.mtx --surf 
> fsaverage rh --cortex --glmdir CAA_CTRL_RH_Age_Sex_Unix.glmdir
>   2. The FSGD file (if using one)
>   3. And the design matrix above
> Attempting to diagnose further
> SumSq: Min=0.00 (col 5), Max=611.699463 (col 4)
>  The scale is much different between columns 5 and 4, you may want to
>  normalize by subtracting the mean and dividing by the standard deviation.
> Column 5,  all values are 0
> Column 6,  all values are 0
> Columns 5 and 6 are the same
>
> I did not get this error when I was only looking at the difference in 
> thickness between the two groups, so I am guessing there is not an 
> issue with the file format? Looking at the log, does this mean that I 
> also need to demean the age variable? I was planning on running some 
> contrasts looking at the interactions between group and age after 
> controlling for sex etc. in order to see if I should go with a DOSS 
> approach, but using those contrasts still gives me the same error.
>
> Thanks for your help!
>
> Best,
> Arsenije
> ---
> *Arsenije Subotic*| MSc Student
> Department of Clinical Neurosciences
> Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada
> Tel: (403) 918-6970
> arsenije.subot...@ucalgary.ca 
>
>
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Re: [Freesurfer] mri_segstats and mris_anatomical_stats read out different # of rois

[Greve, Douglas N.,Ph.D.]

which ROIs are different?

On 2/22/19 5:39 PM, Winkelbeiner, Stephanie A wrote:
>
> External Email - Use Caution
>
> Hi Freesurfers,
>
> I’m trying to read out GM and WM values from parcels (ROIs) but get a 
> different amount of ROIs for GM and WM.
>
> I use the following commands (embedded in a loop),
>
> for GM
>
> mris_anatomical_stats -mgz \
>
>     -cortex label/lh.cortex.label \
>
>     -f stats/lh.250.aparc.pial.stats \
>
>     -b -a 250.aparc \
>
>     -c label/colortable.ctab \
>
>     $subject lh pial
>
> and for WM
>
> mri_segstats \
>
>     --seg mri/vol250.lh.nii.gz \
>
>     --ctab ../fsaverage/colortable.ctab \
>
>     --i $dtipath/$subj/dti_FA.nii.gz \
>
>     --excludeid 0 \
>
>     --empty \
>
>     --sum stats/${subj}_fa_lh.stats
>
> where “../fsaverage/colortable.ctab” has 299 labels and 
> “mri/vol250.lh.nii.gz” is the segmented image that was extended 2mm 
> into the WM and registered to the DTI image.
>
> Is it possible that these two commands read out different amounts of ROIs?
>
> And is there a reason why the –c flag in mris_anatomical_stats doesn’t 
> save the colortable for each subject?
>
> I would be very grateful for some help!
>
> Thanks,
>
> Stephanie
>
>
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Re: [Freesurfer] dt_recon --> tbss

[Greve, Douglas N.,Ph.D.]

no idea. If you want to use tbss, why not use FSL to do the dti analysis 
from the start?

On 2/26/19 10:27 AM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am working through dt_recon troubleshooting  (One subjects 
> registration to anatomical is skewed leading to incorrect masking of 
> that subjects FA image). I would like to use the dt_recon's FA outputs 
> and input them into FSL's tbss pipeline. My question is are there any 
> steps I should take converting or modifying the FA images so they are 
> compatible with the tbss pipeline. My intention was to take the 
> dt_recon fa or fa-masked into the tbss_1_preproc command?
>
> Are there any considerations I should take into account?
>
> Best
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
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Re: [Freesurfer] downsample fsnative

[Greve, Douglas N.,Ph.D.]

please include the previous correspondence in your emails

On 2/26/19 11:33 AM, Ella Hanns wrote:
>
> External Email - Use Caution
>
> Dear Bruce,
>
> Thanks a lot for your help!
>
> I now (roughly) ran the following pipeline but still did not manage to 
> downsample my functional data in fsnative space:
>
>  1. /run mri_vol2surf to map functional data onto fsnative surface/:
>
> My functional data contains one beta coefficient per voxel and 
> represents a strong effect in auditory cortex regions. I see a similar 
> pattern in volume and in surface space.
>
> This the command I run:
>
> mri_vol2surf --hemi $hemi \
>
> --cortex \
>
> --mov $data_path/sub-${subj}_volume_func.nii.gz \
>
> --regheader sub-${subj} \
>
> --out $data_path/sub-${subj}_surface_func _hemi-$hemi.gii \
>
> --projfrac-avg 0.000 1.000 0.200 \
>
> --trgsubject sub-${subj} \
>
> --interp trilinear
>
>  2. /run mri_surf2surf to downsample functional data in fsnative space/:
>
> The number of vertices in the downsampled sphere.reg file matches the 
> number of vertices in the downsampled functional data but all I see 
> when inspecting the data now is noise instead of auditory activation.
>
> This is the command I run to downsample the sphere.reg file 
> (downsampled file is stored in surf folder of dummy subject 9):
>
> mris_decimate -d 0.1 $data_path/surf/$hemi.sphere.reg $dummy_path/ 
> surf/$hemi.sphere.reg
>
> This is the command I run to downsample my functional data:
>
> mri_surf2surf --hemi $hemi \
>
> --srcsubject sub-${subj} \
>
> --srcsurfval sub-${subj}_surface_func_hemi-$hemi.gii \
>
> --trgsubject sub-9 \
>
> --trgsurfval sub-${subj}_surface_func_ds_hemi-$hemi.gii
>
> Does anyone see what might go wrong here?
>
> Any help would be greatly appreciated!
>
> Cheers,
>
> Ella
>
>
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Re: [Freesurfer] Question about fsaverage_sym

[Greve, Douglas N.,Ph.D.]

On 2/26/19 7:58 PM, Alon Baram wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I have subject's surfaces where I first register the rh to the lh 
> using xhemireg, then register both hemispheres to fsaverage_sym using 
> surfreg, and then resample the registered surface to the isocahedron 
> using mris_surf2surf (see code below if that's helpful, part of the 
> RSA toolbox, written by Joern Diedrichsen). This means that for the 
> two hemispheres of these surfaces, each vertex number corresponds to 
> an exact anatomical location (vertex i in rh will be in the exact 
> mirroring location of vertex i).
>
> (I then also move the coordinates of the surface to correspond to 
> world, rather than RAS_tkreg coords, but I think that is irrelevant to 
> my question. This is used to create searchlights ).
>
> I then compute curvature maps on these surfaces, and would like to 
> view them in Freeview overlaid on a common surface. As the remapped 
> surfaces were registered to fsaverage_sym, I thought it would make 
> sense to load them as overlays on the fsaverage_sym surfaces. However 
> I'm not sure on which hemisphere of fsaverage_sym should the curv of 
> the rh be overlaid on. I originally thought it shouldn't matter -  
> that the rh of fsaverage_sym was an exact mirror of the lh, so it 
> shouldn't matter if I load the curv as overlay on the lh or rh. But 
> for a reason I don't understand, that is not true, and it really 
> changes how the curvature looks on the surface.
I can't tell from your code, but you probably registered both lh and rh 
to the lh of fsaveage_sym, so you should only view the results on that. 
If you want us to look at your code, you must give us simple command lines.
> Moreover, it looks exactly the same if I load the curvature as overlay 
> on the rh of fsaverage or fsaverage_sym - I thought these two should 
> be different.
The overlay will be the same since it is the same overlay. If you look 
carefully, you will see that there are some small differences in the 
curvature patterns. fsaverage_sym was created from the same subjects as 
fsaverage, so it is not surprising that they are similar.
>
> What am I getting wrong? which is the correct way of viewing the 
> curvature?
> Thanks very much for the help.
>
> 
>
> function S=freesurfer_mapicosahedron_xhem(subj,subject_dir,varargin);
>
> % function S=freesurfer_mapicosahedron(subj,subject_dir,varargin);
>
> % Resampels a registered subject surface to a regular isocahedron
>
> % This allows things to happen exactly in atlas space - each vertex number
>
> % corresponds exactly to a anatomical location
>
> % Makes a new folder, called ['x' subj] that contains the remapped subject
>
> % Uses function mri_surf2surf
>
> % INPUT:
>
> % subj: subject name
>
> % subjects_dir: freesurfer's SUBJECT_DIR
>
> % VARARGIN:
>
> % 'hemisphere',[1 2]: left / right or both hemispheres
>
> % 'surf_files',{'',''}: Surface files to be resampled
>
> % {'.white','.pial','.inflated','.sphere.reg','.sphere'};
>
> % 'curv_files',{'',''}: Curvature files to be resampled
>
> % {'.curv','.sulc','.area'};
>
> % 'smoothing',1:Smoothing iterations applied (otherwise nearest neighbour)
>
> % ---
>
> % v1.0 Joern Diedrichsen (j.diedrich...@ucl.ac.uk 
> 
>
> %
>
>
> current_dir=pwd;
>
> direct=[getenv('FREESURFER_HOME') filesep 'average' filesep 'surf' ];
>
> old_dir=getenv('SUBJECTS_DIR');
>
> % if (isempty(subject_dir))
>
> %subject_dir=getenv('SUBJECTS_DIR');
>
> % else
>
> %setenv('SUBJECTS_DIR',subject_dir);
>
> % end;
>
> subject_dir=getenv('SUBJECTS_DIR');
>
> structname={'left','right'};
>
> dirname={'LeftHem','RightHem'};
>
> hem={'lh','rh'};
>
> surf_files={'.white','.pial','.inflated'};
>
> curv_files={'.curv','.sulc','.area'};
>
> smoothing=1;
>
> hemisphere=[1:2]; % Do both hemispheres
>
> vararginoptions(varargin,{'smoothing','surf_files','curv_files','hemisphere'});
>
> % read freesurfer version
>
> ver_file = fullfile(getenv('FREESURFER_HOME'),'build-stamp.txt');
>
> if exist(ver_file)
>
> fid = fopen(ver_file);
>
> verStr= fgetl(fid);
>
> fclose(fid);
>
> verStr= strrep(verStr,'-v',' ');
>
> verStr= textscan(verStr,'%s%f');
>
> fsl_ver = verStr{2};
>
> end
>
> new_dir = [subject_dir filesep 'x' subj filesep 'surf'];
>
> if (~exist(new_dir))
>
> mkdir(new_dir);
>
> end;
>
> num_surf=length(surf_files);
>
> files={surf_files{:},curv_files{:}};
>
> for h=hemisphere
>
> % Original subjects dir
>
> if (h==1)
>
> orig_dir =fullfile(subject_dir,subj,'surf');
>
> else
>
> orig_dir =fullfile(subject_dir,subj,'xhemi','surf');
>
> end;
>
> cd(orig_dir);
>
> % [vertex_coords, faces]
>
> [Vico,F]=read_surf([direct filesep 'lh.sphere.reg']); % 
> /opt/fmrib/FreeSurfer_releases/6.0/average/surf/lh.sphere.reg
>
> % Topology file
>
> for i=1:length(files)
>
> if i<=num_surf
>
> % e.g /home/fs0/abaram/scratch/freesurfer-subjects/s99/surf/lh.white
>
> [V]=read_surf([orig_dir 

Re: [Freesurfer] mni152reg

[Greve, Douglas N.,Ph.D.]

did you check the registration? Run mni152reg --help to see how

On 2/26/19 2:36 PM, john Anderson wrote:
>
> External Email - Use Caution
>
> Hi Dr Greve,
>
> I used --regheader to move PET to T1.
> mni152reg in mri_vol2vol as follows:
> mri_vol2vol --mov PET.nii.gz --mni152reg --targ 
> $FSL_DIR/data/standaard/MNI152_2mm_brain.nii.gz --o PET_MNI.nii.gz
>
> this command moved PET to MNI but it crop the image and the 
> orientation is not MNI so Ima not sure what I am doing wrong. Any 
> highlights are appreciated.
>
> My understanding is to move PET to MNI, I need to move PET to T1 then 
> move T1 to MNI the merge the two matrices PET2T1 and T12MNI finally 
> apply warp of PET using this merged matrix but I don't know how I can 
> do it in Freesurfer (if correct).
>
> Thanks for any advice.
> John
>
>
> Why did you use --regheader in vol2vol? You will probably need to do a 
> registration (mri_coreg). Did you check the mni152 reg?
>
> On 2/26/19 10:01 AM, john Anderson wrote:
>
>
>
> ‐‐‐ Original Message ‐‐‐
> On Tuesday, February 26, 2019 10:01 AM, john Anderson 
>  wrote:
>
>> Dear FS experts,
>> I would like to move PET image to MNI152. What is the correct command 
>> to do so. I tried
>> mri_vol2vol --mov PET.nii.gz --s subjID --targ 
>> $SUBJECTS_DIR/subjID/mri/orig.mga --regheader --o PET_T1.nii.gz
>>
>> mni152reg --s subjID
>> then
>> mri_vol2vol --inv --targ PET_T1.nii.gz --mov 
>> $FSL_DIR/data/standard/MNI152_T1_2mm_brain.nii.gz --o 
>> PET_T1_2MNI153_2mm.nii.gz --interp nearest 
>> --reg $SUBJECTS_DIR/subjID/mri/transforms/reg.mni152.reg.dat
>>
>> I still not happy with thresults. PET not perfectly moved to MNI.
>> please are the steps above correct? Can you kindly suggest any ideas 
>> to improve PET registration to MNI?
>>
>> Thanks
>> John
>
>
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Re: [Freesurfer] MD with dt_recon

[Daniel Callow]

External Email - Use Caution

Thank you!
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298


On Thu, Feb 28, 2019 at 2:56 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> sorry, yes, that is right
>
> On 2/27/19 2:18 PM, Daniel Callow wrote:
> >
> > External Email - Use Caution
> >
> > Sorry, I just found in a previous post by doug that ADC is the same as
> MD?
> > *Daniel Callow*
> > /PhD Student, Neuroscience and Cognitive Science/
> > Exercise for Brain Health Lab
> > University of Maryland, College Park
> > _ddcc2...@gmail.com _
> > 443-254-6298
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] MD with dt_recon

[Greve, Douglas N.,Ph.D.]

sorry, yes, that is right

On 2/27/19 2:18 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Sorry, I just found in a previous post by doug that ADC is the same as MD?
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
> ___
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Re: [Freesurfer] MD with dt_recon?

[Greve, Douglas N.,Ph.D.]

Yes

On 2/27/19 2:00 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> There is no mean diffusivity output with dt_recon. How would you 
> suggest to create MD images? Could you simply divide the adc.nii.gz 
> map by 3?
>
> Best,
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
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Re: [Freesurfer] projfrac question

[Greve, Douglas N.,Ph.D.]

I would have thought that it would have changed. Can you look through 
the logs and find the mri_vol2surf command and verify that the 
--projfrac argument is changing?

On 2/28/19 2:51 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> Thank you very much for your reply.
>
> I was actually using -force and It did take a reasonable amount of time.
>
> Then I ran the selxavg command to get the first level maps, and I 
> guess It used the last preprocessd data which was from projfrac 0.2.
>
>
> Thanks
>
> Mona
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Thursday, February 28, 2019 2:41:25 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] projfrac question
> The projfrac function might not be working in the way that you think. It
> might not actually be re-running anything. Did preproc-sess finish
> faster than you would have expected? You can try deleting the projfrac
> output and re-running. You can also run preproc-sess with -force, but
> this will force it to re-run everything. If you want to use multiple
> project fracs, then you should copy the functional tree to a new
> location (if you use -p with cp, it will copy the modification time,
> which will make preproc-sess run faster).
>
> On 2/28/19 12:55 PM, Nasiriavanaki, Zahra wrote:
> >
> > Dear Freesurfers
> >
> >
> > Hi
> >
> > I was trying to look at the activation in different cortical layers in
> > a _single subject_.
> >
> > I ran my preproc-sess command three times, once without using
> > -projfrac flag, once  -projfrac 0.5 and lastly -projfrac 0.2
> >
> > The activation patterns are exactly the same.
> >
> > My voxel sizes are 1.1*1.1*1.1 .
> >
> > My question is:
> >
> > 1-Is it normal that the activations do not change at all the more I
> > get closer to white matter?
> >
> > 2-when I use -projfrac 0.2 , does it mean that I am averaging the
> > activation between white matter layer to 0.2 of gray matter layer? Or
> > is it averaging the activation between pial surface to 0.2 gray matter?
> >
> >
> > I hope my questions are clear.
> >
> >
> > Thanks
> >
> > Mona
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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>
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Re: [Freesurfer] dt_recon and mri_vol2vol issue

[Greve, Douglas N.,Ph.D.]

Did you check the registration? My guess is that the registration failed 
because the initial FSL registration failed. I've put a new version here

https://gate.nmr.mgh.harvard.edu/safelinks/greve/dt_recon

it has a better initializer. Just copy it over the one in 
$FREESURFER_HOME/bin (make a backup of the original one though)

On 2/25/19 1:50 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello freesurfer experts,
>
> I am running dt_recon with the following script
>
> dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i 
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/image01.dcm 
> --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o 
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}.
>
>
> and mri_vol2vol to get the wmparc and aseg.mgz files in my lowb space 
> with the script below
>
> mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz 
> --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/wmparc.mgz --inv 
> --interp nearest --o 
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz
>  
> --reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
>
>
> mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz 
> --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/aseg.mgz --inv 
> --interp nearest --o 
> $subj_dir/dtrecon/${subj}.${cond}./aseg2diff.nii.gz --reg 
> $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
>
>
> However, one of my subjects shows a major issue with the mri_vol2vol 
> registration (for most of the subject scans it seems to work no 
> problem). When looking at the wmparc2diff.mgz I created (screenshot 
> attached), it is apparent that the registration of the wmparc to 
> wmparc2diff space actually causes wmparc2diff.mgz to be further from 
> the lowb than wmparc is. This same registration issue occurs for aseg.mgz.
>
>
> I assume this means there is an issue with the register.dat file for 
> this subject? If so is there any way to troubleshoot the issue and get 
> a correct register.dat file?
>
>
> For reference, the following commands and registration steps have 
> worked for other subjects, as well as this same subject's scans under 
> another condition.
>
>
> Any advice with troubleshooting would be greatly appreciated.
>
>
> Best,
>
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
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Re: [Freesurfer] projfrac question

[Nasiriavanaki, Zahra]

Hi Doug


Thank you very much for your reply.

I was actually using -force and It did take a reasonable amount of time.

Then I ran the selxavg command to get the first level maps, and I guess It used 
the last preprocessd data which was from projfrac 0.2.


Thanks

Mona


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

Sent: Thursday, February 28, 2019 2:41:25 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] projfrac question

The projfrac function might not be working in the way that you think. It
might not actually be re-running anything. Did preproc-sess finish
faster than you would have expected? You can try deleting the projfrac
output and re-running. You can also run preproc-sess with -force, but
this will force it to re-run everything. If you want to use multiple
project fracs, then you should copy the functional tree to a new
location (if you use -p with cp, it will copy the modification time,
which will make preproc-sess run faster).

On 2/28/19 12:55 PM, Nasiriavanaki, Zahra wrote:
>
> Dear Freesurfers
>
>
> Hi
>
> I was trying to look at the activation in different cortical layers in
> a _single subject_.
>
> I ran my preproc-sess command three times, once without using
> -projfrac flag, once  -projfrac 0.5 and lastly -projfrac 0.2
>
> The activation patterns are exactly the same.
>
> My voxel sizes are 1.1*1.1*1.1 .
>
> My question is:
>
> 1-Is it normal that the activations do not change at all the more I
> get closer to white matter?
>
> 2-when I use -projfrac 0.2 , does it mean that I am averaging the
> activation between white matter layer to 0.2 of gray matter layer? Or
> is it averaging the activation between pial surface to 0.2 gray matter?
>
>
> I hope my questions are clear.
>
>
> Thanks
>
> Mona
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] Correcting Defect error

[Greve, Douglas N.,Ph.D.]

That looks pretty awful. You should check the orig.nofix surfaces. I bet 
your data is extremely noisy

On 2/28/19 11:37 AM, Miguel Ángel Rivas Fernández wrote:
>
> External Email - Use Caution
>
>
> Dear Freesurfer devs,
>
>
> I ran the recon-all in one subject and and this process was stopped in 
> the topology correction. In particular during the "CORRECTING DEFECT 
> 36 (vertices=19847, convex hull=5892, v0=94733)". I reviewed the 
> lh.inflated.nofix and the lh.orig.nofix files in Freeview and I 
> noticed that the this error would be located in the lh.inflated.nofix 
> file. How can I fix this problem?
>
> I sent to you a screenshot of the lh.inflated.nofix file as well as 
> the recon-all.log file if you want take a look.
>
>
>
> Best regards,
>
> -- 
> *Miguel Ángel Rivas Fernández*
>
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Re: [Freesurfer] projfrac question

[Greve, Douglas N.,Ph.D.]

The projfrac function might not be working in the way that you think. It 
might not actually be re-running anything. Did preproc-sess finish 
faster than you would have expected? You can try deleting the projfrac 
output and re-running. You can also run preproc-sess with -force, but 
this will force it to re-run everything. If you want to use multiple 
project fracs, then you should copy the functional tree to a new 
location (if you use -p with cp, it will copy the modification time, 
which will make preproc-sess run faster).

On 2/28/19 12:55 PM, Nasiriavanaki, Zahra wrote:
>
> Dear Freesurfers
>
>
> Hi
>
> I was trying to look at the activation in different cortical layers in 
> a _single subject_.
>
> I ran my preproc-sess command three times, once without using 
> -projfrac flag, once  -projfrac 0.5 and lastly -projfrac 0.2
>
> The activation patterns are exactly the same.
>
> My voxel sizes are 1.1*1.1*1.1 .
>
> My question is:
>
> 1-Is it normal that the activations do not change at all the more I 
> get closer to white matter?
>
> 2-when I use -projfrac 0.2 , does it mean that I am averaging the 
> activation between white matter layer to 0.2 of gray matter layer? Or 
> is it averaging the activation between pial surface to 0.2 gray matter?
>
>
> I hope my questions are clear.
>
>
> Thanks
>
> Mona
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] projfrac question

[Nasiriavanaki, Zahra]

Dear Freesurfers


Hi

I was trying to look at the activation in different cortical layers in a single 
subject.

I ran my preproc-sess command three times, once without using -projfrac flag, 
once  -projfrac 0.5 and lastly -projfrac 0.2

The activation patterns are exactly the same.

My voxel sizes are 1.1*1.1*1.1 .

My question is:

1-Is it normal that the activations do not change at all the more I get closer 
to white matter?

2-when I use -projfrac 0.2 , does it mean that I am averaging the activation 
between white matter layer to 0.2 of gray matter layer? Or is it averaging the 
activation between pial surface to 0.2 gray matter?


I hope my questions are clear.


Thanks

Mona

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Re: [Freesurfer] Second order (square) link function for GLM

[Greve, Douglas N.,Ph.D.]

If you wanted to do a simple analysis looking at the effect of age in a 
linear fashion, you'd have a deisgn matrix something like
1 agesubject1
1 agesubject2
...

ie, first column all ones, second column the ages of each subject.
If you think the change is quadratic, then you'd use

1 agesubject1^2
1 agesubject2^2
...

ie, first column all ones, second column the square of the ages of each 
subject.

Then use a contrast [0 1] to test whether the 2nd column regressor is 
diff than 0. (btw, you should demean your ages before squaring)

On 2/28/19 12:12 PM, Abhinav Yadav wrote:
>
> External Email - Use Caution
>
> Hi Douglas,
>
>     Thanks for your reply. I am not sure how to do this with design 
> matrix. I am trying to get higher order fit. Basically I want to see 
> that whether the cortical thickness varies in a quadratic fashion with 
> the behaviour score.
>
>     Are you are suggesting that I should put square root values of the 
> behavioural scores in the design matrix? I am not sure if that is the 
> right approach.
>
>    Looking forward to hearing back from you.
>
> Abhinav
>
> On Wed, 20 Feb 2019, 04:12 Greve, Douglas N.,Ph.D., 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> It sounds like you will just need to create your own design matrix
> and
> then feed it into mri_glmfit with --X (and not include --fsgd)
>
>
> On 2/12/19 12:03 AM, Abhinav Yadav wrote:
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> > I am trying to do GLM analysis for cortical thickness with a
> > behavioral score. I wanted to explore square fit in the GLM.
> Basically
> > wanted to see weather the behaviour is related in a quadratic
> function
> > instead of linear one.
> >
> > Couldn't find any option for this is GLM fit.
> >
> >  I was thinking of feeding a squareroot values of the behavioural
> > parameter in the GLM as an alternative. But not sure weather
> that will
> > work. Please any one can help me with this.
> >
> > Thanks,
> > Abhinav
> >
> > ___
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> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] Second order (square) link function for GLM

[Abhinav Yadav]

External Email - Use Caution

Hi Douglas,

Thanks for your reply. I am not sure how to do this with design matrix.
I am trying to get higher order fit. Basically I want to see that whether
the cortical thickness varies in a quadratic fashion with the behaviour
score.

Are you are suggesting that I should put square root values of the
behavioural scores in the design matrix? I am not sure if that is the right
approach.

   Looking forward to hearing back from you.

Abhinav

On Wed, 20 Feb 2019, 04:12 Greve, Douglas N.,Ph.D., 
wrote:

> It sounds like you will just need to create your own design matrix and
> then feed it into mri_glmfit with --X (and not include --fsgd)
>
>
> On 2/12/19 12:03 AM, Abhinav Yadav wrote:
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> > I am trying to do GLM analysis for cortical thickness with a
> > behavioral score. I wanted to explore square fit in the GLM. Basically
> > wanted to see weather the behaviour is related in a quadratic function
> > instead of linear one.
> >
> > Couldn't find any option for this is GLM fit.
> >
> >  I was thinking of feeding a squareroot values of the behavioural
> > parameter in the GLM as an alternative. But not sure weather that will
> > work. Please any one can help me with this.
> >
> > Thanks,
> > Abhinav
> >
> > ___
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> > Freesurfer@nmr.mgh.harvard.edu
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>
>
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Re: [Freesurfer] problem with tkregister

[Greve, Douglas N.,Ph.D.]

need more info

On 2/27/19 9:42 AM, Barletta, Valeria wrote:
>
> Dear Freesurfers,
>
> I am trying to do a registration with tkregister but am experiencing 
> this type of issue:
>
>
> The image I should fit is the sagittal view instead of coronal.
>
> Is there some way to change it to coronal from the command window? Any 
> other option?
>
> Thank you very much,
>
> Vale
>
>
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Re: [Freesurfer] Beta extraction

[Greve, Douglas N.,Ph.D.]

The betas are averages across subject, so you should not get one for 
each subject

On 2/27/19 4:34 PM, Jahan, Bushra wrote:
>
> When I ran the following command (with our data), I got the average 
> beta values for each segmentation i.e. only 5 beta values (as opposed 
> to 5 beta values for each subject).
>
>
> mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf
> beta.clusters.dat
>
>
> That said, is it necessarily to run the previous command for each 
> subject  (in order to extract 5 beta values for each subject) or is 
> there way to extract betas for each subject from the group analysis?
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Thursday, November 29, 2018 11:19:33 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Beta extraction
> Use something like
> mri_segstats --seg ocn.mgh --i beta.mgh --excludeid 0 --avgwf
> beta.clusters.dat
>
> See mri_glmfit-sim --help for more info on the OCN file and mri_segstats
> --help for info on the avgwf file
>
>
> On 11/29/2018 04:40 PM, Jahan, Bushra wrote:
> > I am wondering how to extract beta values from the clusters of task
> > functional data, particularly output of the multiple comparisons
> > correction?
> >
> > Aava Jahan
> >
> >
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>
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Re: [Freesurfer] mri_coreg error

[Greve, Douglas N.,Ph.D.]

it says it cannot find /XYZ/2123.nii
probably this file does not exist

On 2/28/19 10:09 AM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> Hi FreeSurfer community,
>
> when I run mri_coreg I get the following error.
>  /XYZ/2123/mri/brainmask.mgz is in the specified location.
>
> Can you help me with this?
>
> Thanks!
> Boris
>
> mri_coreg --s 2123 --mov /XYZ/2123.nii --reg 2123.reg.lta
> Could not set locale
> No such file or directory
> Could not set locale
>
> $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
> cwd /home/demenzbild
> cmdline mri_coreg --s 2123 --mov /XYZ/2123.nii --reg 2123.reg.lta
> sysname  Linux
> hostname XXX
> machine  x86_64
> user     d
> dof    6
> nsep    2
> cras0    1
> ftol    0.00
> linmintol    0.001000
> bf       1
> bflim    30.00
> bfnsamp    30
> SmoothRef 0
> SatPct    99.99
> MovOOB 0
> optschema 1
> Reading in mov /XYZ/2123.nii
> WARNING: 78694 NaNs found in volume /XYZ/2123.nii...
>
> No such file or directory
> Reading in ref /XYZ/2123/mri/brainmask.mgz
> mghRead(/XYZ/2123/mri/brainmask.mgz, -1): could not open file
>
>
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[Freesurfer] mri_coreg error

[Boris Rauchmann]

External Email - Use Caution

Hi FreeSurfer community,

when I run mri_coreg I get the following error.
 /XYZ/2123/mri/brainmask.mgz is in the specified location.

Can you help me with this?

Thanks!
Boris

mri_coreg --s 2123 --mov /XYZ/2123.nii --reg 2123.reg.lta
Could not set locale
No such file or directory
Could not set locale

$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
cwd /home/demenzbild
cmdline mri_coreg --s 2123 --mov /XYZ/2123.nii --reg 2123.reg.lta
sysname  Linux
hostname XXX
machine  x86_64
user d
dof6
nsep2
cras01
ftol0.00
linmintol0.001000
bf   1
bflim30.00
bfnsamp30
SmoothRef 0
SatPct99.99
MovOOB 0
optschema 1
Reading in mov /XYZ/2123.nii
WARNING: 78694 NaNs found in volume /XYZ/2123.nii...

No such file or directory
Reading in ref /XYZ/2123/mri/brainmask.mgz
mghRead(/XYZ/2123/mri/brainmask.mgz, -1): could not open file
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