[Freesurfer] mri_glmfit-sim cluster correction threshold inquiry

[Arsenije Subotic]

External Email - Use Caution

Hello,

I am planning on running a correction for multiple comparisons, and I was 
hoping to use a vertex wise cluster forming threshold of 1.3, however after 
reading more when I ran the mri_glmfit-sim —help command it recommends using 
the permutation test if you are planning on using 1.3 as a threshold. Is there 
any reason why it is not recommended to use the 1.3 cluster threshold? My study 
is fairly exploratory so I was hoping to be a bit more lenient when it comes to 
adjusting the threshold.

Thanks!
Arsenije

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

[Sparsh Jain]

External Email - Use Caution

I see. How may I check that?

Sparsh

On Thu, Mar 7, 2019 at 6:42 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Is that point labeled as WM in the aseg? If so, then it is not a problem
> with matlab:)
>
> On 3/7/19 5:58 PM, Sparsh Jain wrote:
> >
> > External Email - Use Caution
> >
> > Thanks a lot! It worked.
> > While most of the labels were correct, the matlab script returned the
> > wrong location for one point . The script returned the label 'right
> > cerebral white matter' for a point that seems to lie in the middle of
> > the right amygdala. I have attached the screenshots. I do not think
> > that there is a white matter area close enough to confuse the script.
> > Could you tell me why this may have occurred?
> > When I write the line "crs = round(inv(aparcaseg.tkrvox2ras)*[tkr tka
> > tks 1]')+1" , is there an error due to rounding in the conversion?
> >
> > I was planning to inflate a sphere around each electrode point and get
> > the neighboring anatomical regions as well.
> >
> > Sparsh
> >
> > On Thu, Feb 21, 2019 at 12:51 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > For a volume, I would do it differently. In matlab
> >
> > [segcodes segnames ] = read_fscolorlut(); % read in the seg lookup
> > table
> >
> > aparcaseg = MRIread('aparc+aseg.mgz'); % Load in the volume
> > crs = round(inv(aparcaseg.tkrvox2ras)*[tkr tka tks 1]')+1; % convert
> > your tkreg coords to col, row, and slice
> > c = crs(1);
> > r = crs(2);
> > s = crs(3);
> > segno = aparcaseg.vol(r,c,s); % extract the segmentation number
> > ind = find(segno == segcodes); % convert to the ne name of the
> > segmentation
> > segname = segnames(ind,:)
> >
> >
> > On 2/20/19 9:58 AM, Sparsh Jain wrote:
> > >
> > > External Email - Use Caution
> > >
> > > Hi Doug,
> > >
> > > I tried what you suggested, but it did not work (see below for
> > details
> > > of what we tried). We have TkReg RAS coordinates (or vertex points)
> > > for our electrode contacts; most contacts are _deep within the
> > > brain_ (e.g., hippocampus and amygdala). We want to get a
> > variable in
> > > Matlab that will give us the anatomical labels as a function of the
> > > TkReg RAS coordinates (or vertex points). How can we do this?
> > >
> > > Thanks!
> > >
> > > Sparsh
> > >
> > > _What I tried:_ I read the 'rh.aparc.2009a.annot' file in matlab
> > using
> > > read_annotation.m. That gave me 76 labels for right hemisphere,
> > which
> > > I believe correspond to the surface parcellations only. In
> > freeview I
> > > loaded the orig.mgz, aparc.a2009s+aseg.mgz, rh.pial and
> > rh.inflated. I
> > > then clicked on a cortical surface point to see if I can get the
> > > corresponding vertex number or structure ID. On doing so, I found a
> > > value in the Vertex row under rh.pial of freeview but this number
> > > wasn't found in the matlab output (in the colortable.label or
> > > colortable.table). I think I am looking in the wrong place to
> > find the
> > > vertex # on freeview.
> > >
> > > Also, I did not find a readable file for the segmentation data. I
> > > tried to read the aparc.a2009s+aseg.mgz on Matlab but that
> > didn't work.
> > > Show quoted text
> > >
> > > On Thu, 7 Feb 2019, 16:10 Greve, Douglas N.,Ph.D.
> > > mailto:dgr...@mgh.harvard.edu>
> > >
> wrote:
> > >
> > > First, you'll have to find the closest vertex for each point in
> > > fsavarage. You can do this with by creating a label file
> > then using
> > > mri_label2label with the --paint option.
> > >
> > > To find the label associated with each vertex, it is  probably
> > > easiest
> > > to use matlab using read_surf.m and read_annotation.m
> > >
> > > On 2/5/19 11:17 AM, Sparsh Jain wrote:
> > > >
> > > > External Email - Use Caution
> > > >
> > > > Good afternoon
> > > >
> > > > Is there is way to automatically extract the anatomical
> > locations
> > > > corresponding to a set of RAS coordinates using Freesurfer's
> > > atlas? I
> > > > have a set of 200 points and I am trying to get their
> > anatomical
> > > > labels automatically.
> > > >
> > > > Thank you
> > > > Sparsh
> > > >
> > > > ___
> > > > Freesurfer mailing list
> > > > Freesurfer@nmr.mgh.harvard.edu
> > 
> > >  > >
> > > > 

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

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

Is that point labeled as WM in the aseg? If so, then it is not a problem 
with matlab:)

On 3/7/19 5:58 PM, Sparsh Jain wrote:
>
> External Email - Use Caution
>
> Thanks a lot! It worked.
> While most of the labels were correct, the matlab script returned the 
> wrong location for one point . The script returned the label 'right 
> cerebral white matter' for a point that seems to lie in the middle of 
> the right amygdala. I have attached the screenshots. I do not think 
> that there is a white matter area close enough to confuse the script. 
> Could you tell me why this may have occurred?
> When I write the line "crs = round(inv(aparcaseg.tkrvox2ras)*[tkr tka 
> tks 1]')+1" , is there an error due to rounding in the conversion?
>
> I was planning to inflate a sphere around each electrode point and get 
> the neighboring anatomical regions as well.
>
> Sparsh
>
> On Thu, Feb 21, 2019 at 12:51 PM Greve, Douglas N.,Ph.D. 
> mailto:dgr...@mgh.harvard.edu>> wrote:
>
> For a volume, I would do it differently. In matlab
>
> [segcodes segnames ] = read_fscolorlut(); % read in the seg lookup
> table
>
> aparcaseg = MRIread('aparc+aseg.mgz'); % Load in the volume
> crs = round(inv(aparcaseg.tkrvox2ras)*[tkr tka tks 1]')+1; % convert
> your tkreg coords to col, row, and slice
> c = crs(1);
> r = crs(2);
> s = crs(3);
> segno = aparcaseg.vol(r,c,s); % extract the segmentation number
> ind = find(segno == segcodes); % convert to the ne name of the
> segmentation
> segname = segnames(ind,:)
>
>
> On 2/20/19 9:58 AM, Sparsh Jain wrote:
> >
> > External Email - Use Caution
> >
> > Hi Doug,
> >
> > I tried what you suggested, but it did not work (see below for
> details
> > of what we tried). We have TkReg RAS coordinates (or vertex points)
> > for our electrode contacts; most contacts are _deep within the
> > brain_ (e.g., hippocampus and amygdala). We want to get a
> variable in
> > Matlab that will give us the anatomical labels as a function of the
> > TkReg RAS coordinates (or vertex points). How can we do this?
> >
> > Thanks!
> >
> > Sparsh
> >
> > _What I tried:_ I read the 'rh.aparc.2009a.annot' file in matlab
> using
> > read_annotation.m. That gave me 76 labels for right hemisphere,
> which
> > I believe correspond to the surface parcellations only. In
> freeview I
> > loaded the orig.mgz, aparc.a2009s+aseg.mgz, rh.pial and
> rh.inflated. I
> > then clicked on a cortical surface point to see if I can get the
> > corresponding vertex number or structure ID. On doing so, I found a
> > value in the Vertex row under rh.pial of freeview but this number
> > wasn't found in the matlab output (in the colortable.label or
> > colortable.table). I think I am looking in the wrong place to
> find the
> > vertex # on freeview.
> >
> > Also, I did not find a readable file for the segmentation data. I
> > tried to read the aparc.a2009s+aseg.mgz on Matlab but that
> didn't work.
> > Show quoted text
> >
> > On Thu, 7 Feb 2019, 16:10 Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>
> > wrote:
> >
> >     First, you'll have to find the closest vertex for each point in
> >     fsavarage. You can do this with by creating a label file
> then using
> >     mri_label2label with the --paint option.
> >
> >     To find the label associated with each vertex, it is  probably
> >     easiest
> >     to use matlab using read_surf.m and read_annotation.m
> >
> >     On 2/5/19 11:17 AM, Sparsh Jain wrote:
> >     >
> >     > External Email - Use Caution
> >     >
> >     > Good afternoon
> >     >
> >     > Is there is way to automatically extract the anatomical
> locations
> >     > corresponding to a set of RAS coordinates using Freesurfer's
> >     atlas? I
> >     > have a set of 200 points and I am trying to get their
> anatomical
> >     > labels automatically.
> >     >
> >     > Thank you
> >     > Sparsh
> >     >
> >     > ___
> >     > Freesurfer mailing list
> >     > Freesurfer@nmr.mgh.harvard.edu
> 
> >      >
> >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >     ___
> >     Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> 
>  >
> > 

Re: [Freesurfer] Extraction of anatomical locations using Matlab

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

Can you include the previous emails so we have context?

On 3/7/19 6:16 PM, Sparsh Jain wrote:
>
> External Email - Use Caution
>
> Good evening.
>  Thanks a lot for the help. It worked !
> While most of the labels were correct, the matlab script returned the 
> wrong location for one point . The script returned the label 'right 
> cerebral white matter' for a point that seems to lie in the middle of 
> the right amygdala. I have attached the screenshots. I do not think 
> that there is a white matter area close enough to confuse the script. 
> Could you tell me why this may have occurred?
> When I write the line "crs = round(inv(aparcaseg.tkrvox2ras)*[tkr tka 
> tks 1]')+1" ,  is there an error due to rounding in the conversion?
>
> I was planning to inflate a sphere around each electrode point and get 
> the neighboring anatomical regions as well.
>
> Sparsh
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] projfrac question

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

Can you try it again? this time use -projfrac 0.2 pf020  (ie, add 
"pf020" after 0.2). Then when you use mkanalysis-sesss, add -expkey 
pf020 to the command line. The pf020 will be included in the output file 
name to make it unique. This allows you to use a single project folder 
(ie, you don't need to copy to a new folder).

On 3/7/19 12:20 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> Thank you very much for your reply.
>
> I ran one of my subjects with the command below and I got this error:
>
> preproc-sess.test -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 
> -surface fsaverage lhrh -fsd bold -d $dir/all_subjects -force
>
> Does it mean I should run it with expert option flag?like the one in 
> recon-all?
>
>
> Thu Mar  7 10:10:00 EST 2019
> mc-sess completed SUCCESSFULLY
> inul_reunpack To Surface -
> rawfunc2surf-sess -fwhm 0 -s inul_reunpack -d 
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects -fsd bold 
> -trgsubject fsaverage -per-run -projfrac 0.2
> ERROR: experts key needed (-expkey)
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Greve, Douglas 
> N.,Ph.D. 
> *Sent:* Wednesday, March 6, 2019 7:06:44 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] projfrac question
> This does appear to be a bug. Are you using FS version 6? If so, I put a
> test in that distriubtion called preproc-sess.test. Can you try running
> that on a subject and see if you get the desired behavior?
>
> On 3/6/19 1:31 PM, Nasiriavanaki, Zahra wrote:
> >
> > Hi Doug
> >
> >
> > I re-analyzed one of my subjects from the very beginning with
> > -projfrac 0.2. But still, in mri_vol2surf, the projfrac is 0.5 (copied
> > below). Could you please let me know what I'm doing wrong?
> >
> > Here is my command:
> >
> > preproc-sess -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 -surface
> > fsaverage lhrh -fsd bold -d $dir/all_subjects -force
> >
> >
> > Thanks
> >
> > Mona
> >
> >
> > mri_vol2surf --mov
> > 
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
> > --reg
> > 
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
> > --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
> > 
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
> > --noreshape --cortex --surfreg sphere.reg
> > srcvol =
> > 
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
> > srcreg =
> > 
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = rh
> > trgsubject = fsaverage
> > surfreg = sphere.reg
> > ProjFrac = 0.5
> > thickness = thickness
> > reshape = 0
> > interp = trilin
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > Done loading volume
> > Input reg is LTA
> >
> >
> >
> > *Zahra (Mona) Nasiriavanaki*
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Center for Biomedical Imaging
> >
> > Massachusetts General Hospital
> >
> > 149 13th Street, 149-2615
> >
> > Charlestown, MA, USA, 02129
> >
> >
> >
> > 
> > *From:* Nasiriavanaki, Zahra
> > *Sent:* Friday, March 1, 2019 11:52:21 AM
> > *To:* freesurfer@nmr.mgh.harvard.edu
> > *Subject:* Re: [Freesurfer] projfrac question
> >
> > Yes, I found it.
> >
> > I should mention that, this log file is the result of today's
> > preprocessing  (-projfrac 0.2) which I did in a separate folder, with
> > all the previous preprocessing files being deleted.
> >
> > As you see the -projfrac is still 0.5 !
> >
> >
> >   Fri Mar  1 11:32:16 EST 2019
> > mri_vol2surf --mov
> > 
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
> > --reg
> > 
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
> > --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
> > 
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
> > --noreshape --cortex --surfreg sphere.reg
> > srcvol =
> > 
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
> > srcreg =
> > 
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = rh
> > trgsubject = fsaverage
> > surfreg = sphere.reg
> > ProjFrac = 0.5
> > thickness = 

Re: [Freesurfer] regions of Yeo 17 networks in fast

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

You have to convert the annotation to a volume using mri_aparc2aseg 
(look at recon-all.log for an example, but note that you'll need to 
specify the output so that it does not overwrite). You'll then need to 
look in the output segmentation and see what the segmentation ids are

On 3/7/19 4:13 PM, std...@virgilio.it wrote:
>
> External Email - Use Caution
>
> Hi list,
>
> I'd like to use the regions included in Yeo 17 networks 
> (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering).
>  
>
> in FS-FAST.
>
> Which is the command line to be used to create a segmentation in 
> $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like 
> to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
>
> Thanks
>
> Stefano
>
>
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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

[Arsenije Subotic]

External Email - Use Caution

Hi Doug,

I realized this error a couple of days ago and now it works.

Thank you,
Arsenije


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Re: [Freesurfer] Accounting for family relation in FS

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

Sorry for the delay ...

This looks like a fairly complicated design, and I'm not sure how to 
think about it. What do you actually want to test in the end?

BTW, the FSGD file you have there will not work. The variables are for 
continuous variables (eg, age) and not discrete variables (eg, sex or 
Pair_no).



On 3/7/19 1:54 AM, Julian Macoveanu wrote:
>
> External Email - Use Caution
>
> Dear FS List,
>
> (apologies for reposting under different title)
>
> I wanted to check if my GLM design for a surface based analysis is 
> sound. I am new to FS so please don’t skip over details.
>
> I have 3 groups of monozygotic twins: low-risk, high-risk, ill. Twin 
> pairs may be present in the same group (e.g both are in the low-risk) 
> or between groups (one of them in high-risk one in affected).  Not all 
> twins have their co-twin in the analysis though.
>
> In order to account for with-pair variance correlation I was wondering 
> if this FSGD example with 9 subjects might do it or if there might be 
> better options.
>
> GroupDescriptorFile 1
> Title …
> Class LR
> Class HR
> Class ILL
> Variables    age sex TIV  Pair_no1 Pair_no2 Pair_no3
> Input subject1 LR  30 M 123456 1 0 0
> Input subject2 LR  30 M 123456 1 0 0
> Input subject3 LR  23 F 123456 0 0 0
> Input subject4 HR  20 F 123456 0 1 0
> Input subject5 HR  21 F 123456 0 0 1
> Input subject6 HR  22 M 123456 0 0 0
> Input subject7 ILL 20 F 123456 0 1 0
> Input subject8 ILL 21 F 123456 0 0 1
> Input subject9 ILL 35 F 123456 0 0 0
>
> I do have 60+ pairs so it will be a lot of variables. I know that PALM 
> has an options to provide an exchangeability file, but FsPalm seems to 
> perform corrections for multiple comparisons only.
>
> Julian
>
>
>
>
> ___
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[Freesurfer] regions of Yeo 17 networks in fast

[stdp82]

External Email - Use Caution

Hi list,

I'd like to use the regions included in Yeo 17 networks 
(https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering).
in FS-FAST.

Which is the command line to be used to create a segmentation in 
$SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it 
to run fcseed-config, specify -seg yourseg.mgz -segid).

Thanks

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Re: [Freesurfer] Gray matter segmentation

[Maxime Perron]

External Email - Use Caution

Hi Greve,

I uploaded my data to the ftp site,

Thanks,
Maxime 

De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Greve, Douglas N.,Ph.D. 

Envoyé : 6 mars 2019 18:26
À : freesurfer@nmr.mgh.harvard.edu
Objet : Re: [Freesurfer] Gray matter segmentation

Can you tar up and upload the subjects to
ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming
Let me know when they are there

On 3/4/19 4:59 PM, Maxime Perron wrote:
>
> External Email - Use Caution
>
> Hi Freesurfer Experts,
>
>
> I was wondering if you have had time to look at my problem?
>
>
> Cheers,
>
> Maxime
>
> 
> *De :* Maxime Perron
> *Envoyé :* 26 février 2019 14:26
> *À :* Freesurfer support list
> *Objet :* Re: [Freesurfer] Gray matter segmentation
>
> Hi Bruce,
>
> Thanks a lot for your quick answer. In the aseg, the gray matter in
> this region is not labelled. I've attached two cases of such error in
> the participants.
>
> In the first participant (S156), the cc seems to be O.K., yet the gray
> matter is not labelled. I tried to correct the aseg but the
> segmentation doesn’t change: indeed, the modification does not seem to
> have been taken into account after the recon-all -noaseg, even after
> modifying both the aseg and the aseg.presurf.
>
> In the second participant (S115), the cc is mislabelled, and it’s
> probably what causes the error of segmentation and gray matter labelling.
>
> All in all, I have two patterns of error. Do you have any
> modifications in mind that could solve these issues?
>
> Thank you very much in all cases!
>
> Maxime
>
>
>
>> On Feb 24, 2019, at 8:14 PM, Bruce Fischl > > wrote:
>>
>> Hi Maxime
>>
>> what does the aseg look like in that region? The pial surface gets
>> "frozen" adjacent to the cc (so it is fixed to be in the same
>> location as the white). Maybe the cc if off by a bit?
>>
>> cheers
>> Bruce
>> On Sat, 23 Feb 2019, Maxime Perron wrote:
>>
>>> External Email - Use Caution
>>> Dear Freesurfer experts,
>>>
>>> I use Freesurfer 6 on macOS Sierra 10.12.6. I noticed a potential
>>> error in some of my participants. In
>>> fact, there seems to have an error in the segmentation of gray
>>> matter. You will find attached pictures
>>> of the segmentation. I am wondering if it is an error and if anyone
>>> has any idea to fix it. I think it
>>> affects the surfaces.
>>> ​
>>> Thank you,
>>> Maxime Perron
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>
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Re: [Freesurfer] projfrac question

[Nasiriavanaki, Zahra]

Hi Doug


Thank you very much for your reply.

I ran one of my subjects with the command below and I got this error:

preproc-sess.test -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 -surface 
fsaverage lhrh -fsd bold -d $dir/all_subjects -force

Does it mean I should run it with expert option flag?like the one in recon-all?


Thu Mar  7 10:10:00 EST 2019
mc-sess completed SUCCESSFULLY
inul_reunpack To Surface -
rawfunc2surf-sess -fwhm 0 -s inul_reunpack -d 
/autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects -fsd bold 
-trgsubject fsaverage -per-run -projfrac 0.2
ERROR: experts key needed (-expkey)



Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129




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

Sent: Wednesday, March 6, 2019 7:06:44 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] projfrac question

This does appear to be a bug. Are you using FS version 6? If so, I put a
test in that distriubtion called preproc-sess.test. Can you try running
that on a subject and see if you get the desired behavior?

On 3/6/19 1:31 PM, Nasiriavanaki, Zahra wrote:
>
> Hi Doug
>
>
> I re-analyzed one of my subjects from the very beginning with
> -projfrac 0.2. But still, in mri_vol2surf, the projfrac is 0.5 (copied
> below). Could you please let me know what I'm doing wrong?
>
> Here is my command:
>
> preproc-sess -s $subj -per-run -nostc -fwhm 0 -projfrac 0.2 -surface
> fsaverage lhrh -fsd bold -d $dir/all_subjects -force
>
>
> Thanks
>
> Mona
>
>
> mri_vol2surf --mov
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
> --reg
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
> --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
> --noreshape --cortex --surfreg sphere.reg
> srcvol =
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/fmcpr.nii.gz
> srcreg =
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_reunpack/bold/024/register.dof6.lta
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = rh
> trgsubject = fsaverage
> surfreg = sphere.reg
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = trilin
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Input reg is LTA
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
> 
> *From:* Nasiriavanaki, Zahra
> *Sent:* Friday, March 1, 2019 11:52:21 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] projfrac question
>
> Yes, I found it.
>
> I should mention that, this log file is the result of today's
> preprocessing  (-projfrac 0.2) which I did in a separate folder, with
> all the previous preprocessing files being deleted.
>
> As you see the -projfrac is still 0.5 !
>
>
>   Fri Mar  1 11:32:16 EST 2019
> mri_vol2surf --mov
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
> --reg
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
> --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi rh --o
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.sm0.fsaverage.rh.nii.gz
> --noreshape --cortex --surfreg sphere.reg
> srcvol =
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/fmcpr.nii.gz
> srcreg =
> /autofs/space/oprah_001/users/jvm27/looming/7T/all_subjects/inul_loom2_7T/bold/024/register.dof6.lta
> srcregold = 0
> srcwarp unspecified
> surf = white
> hemi = rh
> trgsubject = fsaverage
> surfreg = sphere.reg
> ProjFrac = 0.5
> thickness = thickness
> reshape = 0
> interp = trilin
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Input reg is LTA
>
>
> 
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu
>  on behalf of Greve, Douglas
> N.,Ph.D. 
> *Sent:* Friday, March 1, 2019 11:09:30 AM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] projfrac question
> that is part of the bbregister command. Can you find the commands
> related to mri_vol2surf?
>
> On 2/28/19 3:51 PM, Nasiriavanaki, Zahra wrote:
>>
>> 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.
>>
>>

Re: [Freesurfer] PETSurfer: Equivalence between surfaces un gtmseg space and native surface?

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

The surface resolution is set during the recon-all analysis and is 
uninfluenced by the PET data

On 3/7/19 3:16 AM, Matthieu VANHOUTTE wrote:
>  External Email - Use Caution
>
> Ok so if I well understand surface in the gtmseg space would not have
> finer resolution than surface in native space (big voxel)?
>
> On 06/03/2019 23:48, Greve, Douglas N.,Ph.D. wrote:
>> I don't think so. The surfaces are at about 1mm resolution, which should
>> be fine for this. The reason that RBV had to be upsampled is that there
>> is no way to represent the different tissue types at a single (big) voxel
>>
>> On 3/6/19 4:46 PM, Matthieu Vanhoutte wrote:
>>>   External Email - Use Caution
>>>
>>> Dear Douglas,
>>>
>>> RBV PVC use the advantage of upsampled gtmseg space at 0.5 mm3 to
>>> compute PVCorrected images. Would it be beneficial to project this
>>> PVCorrected images onto gtmseg space surfaces to keep this upsampled
>>> resolution ?
>>>
>>> Or would it be equivalent to project these PVCorrected images on
>>> gtmseg space onto native surfaces using --reg rbv2anat.lta ?
>>>
>>> Best,
>>> Matthieu
>>>
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Re: [Freesurfer] Creating Labels

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

Try mri_surfcluster

On 3/6/19 10:03 PM, Jahan, Bushra wrote:
> Hello,
>
> I am wondering how to generate a label in FreeSurfer from peak 
> activation in a cluster - is there a specific command?
>
> Thank you.
>
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Re: [Freesurfer] Resampling a gifti image to nifti using mri_surf2vol fails

[Bruce Fischl]

Hi Bastien

can you send us the full command lines and screen output of whatever you 
have run?


cheers
Bruce
On Thu, 7 Mar 2019, CAGNA Bastien wrote:



External Email - Use Caution

Hi,

First I tried to use my original mask which is a gifti with a single darray as 
NIFTI_INTENT_ESTIMATE that
contains 0 or 1 for each vertex.

But I got it:

"

** DA[0] has coordsys with intent NIFTI_INTENT_ESTIMATE (should be 
NIFTI_INTENT_POINTSET)
MRISreadGiftiAsMRI: no overlay data found in file [filename]

"


So I changed darray to a new one that contains only the list of the point 
coordinates where my mask is
equal to 1 (and use NIFTI_INTENT_POINTSET) and now I have only this error:

" MRISreadGiftiAsMRI: no overlay data found in file [filename] "


Bastien


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Re: [Freesurfer] Resampling a gifti image to nifti using mri_surf2vol fails

[CAGNA Bastien]

External Email - Use Caution

Hi,

First I tried to use my original mask which is a gifti with a single darray as 
NIFTI_INTENT_ESTIMATE that contains 0 or 1 for each vertex.

But I got it:

"

** DA[0] has coordsys with intent NIFTI_INTENT_ESTIMATE (should be 
NIFTI_INTENT_POINTSET)
MRISreadGiftiAsMRI: no overlay data found in file [filename]

"


So I changed darray to a new one that contains only the list of the point 
coordinates where my mask is equal to 1 (and use NIFTI_INTENT_POINTSET) and now 
I have only this error:

" MRISreadGiftiAsMRI: no overlay data found in file [filename] "


Bastien
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Re: [Freesurfer] PETSurfer: Equivalence between surfaces un gtmseg space and native surface?

[Matthieu VANHOUTTE]

External Email - Use Caution

Ok so if I well understand surface in the gtmseg space would not have 
finer resolution than surface in native space (big voxel)?

On 06/03/2019 23:48, Greve, Douglas N.,Ph.D. wrote:
> I don't think so. The surfaces are at about 1mm resolution, which should
> be fine for this. The reason that RBV had to be upsampled is that there
> is no way to represent the different tissue types at a single (big) voxel
>
> On 3/6/19 4:46 PM, Matthieu Vanhoutte wrote:
>>  External Email - Use Caution
>>
>> Dear Douglas,
>>
>> RBV PVC use the advantage of upsampled gtmseg space at 0.5 mm3 to
>> compute PVCorrected images. Would it be beneficial to project this
>> PVCorrected images onto gtmseg space surfaces to keep this upsampled
>> resolution ?
>>
>> Or would it be equivalent to project these PVCorrected images on
>> gtmseg space onto native surfaces using --reg rbv2anat.lta ?
>>
>> Best,
>> Matthieu
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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