[Freesurfer] 回复： unable to map surface to fsaverage4

[Chenfei YE]

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Yes, it solved my problem. Thank you Greve.
Hope next FS version will fix this bug.


Best,
Chenfei


-- 原始邮件 --
发件人: "Greve, Douglas N.,Ph.D.";
发送时间: 2019年3月7日(星期四) 凌晨2:30
收件人: "freesurfer@nmr.mgh.harvard.edu";

主题: Re: [Freesurfer] unable to map surface to fsaverage4




This is a bug in mris_preproc. I have created a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc
Copy this to $FREESURFER_HOME/bin (after making a backup of the one that 
is there)
let us know if this works


On 3/2/19 8:57 AM, Chenfei YE wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I'm following the process described in https://www.cloudneuro.org/ to 
> predict age based on cortical thickness of an individual brain.
> I cannot map surface to the fsaverage4 template by the 2nd command:
>
> recon-all -s subject.id -qcache -target fsaverage4
>
> The error was shown like
>
> mri_surf2surf: could not read su​rface
> ./test2/surf/lh.fsaverage4.sphere.reg
>
> No such file or directory
>
> I tried to change the 1st command like:
>
> recon-all -i input_image -s subject.id -all -target fsavearge4
>
> But still the same error.
>
> My FreeSurfer version is 6.0.0. Maybe that's why I cannot successfully 
> run the code in https://www.cloudneuro.org/. But is there any way to 
> solve this problem? Thank you.
>
> Chenfei
>
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[Freesurfer] Accounting for family relation in FS

[Julian Macoveanu]

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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
Variablesage 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] Creating Labels

[Jahan, Bushra]

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] projfrac question

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

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.
>>
>>
>> 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 
>> 

Re: [Freesurfer] PETSurfer and thickness data

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

Procedurally, you would create stacks (eg, mris_preproc) of the 
thickness and the PET data, then you would use one as the --y input to 
mri_glmfit and the other as --pvr input (in addition to your fsgd file 
or design matrix). The PVR is per-voxel regresssor, so it will create a 
design matrix for each voxel using the data found in the pvr.

Theoretically, you might run into problems because the partial volume 
effect will interact with thickness, so, depending on the nature of the 
PET tracer,  it may be hard to know whether you are seeing a true effect 
or an artifact or it could make a true effect disappear.

On 3/5/19 5:56 PM, Boris Rauchmann wrote:
>  External Email - Use Caution
>
> Dear FS community,
>
> I would like to assess how PET tracer uptake is related to thickness changes 
> in AD patients. Is it possible to generate difference maps for both methods 
> and run a GLM? Or would you suggest another approach?
>
> Thanks,
> Boris
>
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Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08

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

Your FSGD file is incorrect in several ways. Under "variables" you have 
"Sex" and list "Male" and "Female". The variables must be numbers, not 
strings. The variables should also represent continuous quantities, not 
categories. To handle sex, you should have a total of 6 categories, the 
3 that you have divided into male an female.

On 3/5/19 12:51 PM, Arsenije Subotic wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I am still struggling to examine differences in thickness using the 
> command line stream for my two groups after controlling for age and 
> sex. I get the following error when running the command line:
>
> 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
>
>
>
> My design matrix is:
> 1 -1 0 0 0 0 (Examining difference in thickness after controlling for effects
> of age and sex)
>
> I’ve also attached the FSGD file that I’ve been using. Please let 
> me know if there is something wrong with the file (although I have 
> used a similar file without the covariates and did not have any issues).
>
> Thanks!
> 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] Masks in mri_segstats

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

Only one mask and one threshold is used. If you need to combine masks in 
some way, you can use fscalc (or mri_binarize).



On 3/5/19 12:47 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer experts,
>
> I would like to use mri_segstats with two different masks and 
> thresholds, such as:
>
> mri_segstats --mask mask1 --maskthresh thresh1 --mask mask2 
> --maskthresh thresh2
>
> This command can run smoothly with our any error. However, I am not 
> clear if the results are correct. I mean if mri_segstats uses the 
> overlap between two masks or only uses the last input mask and 
> threshold? Any suggestions?
>
> Thank you and best regards,
>
> Lizhi
>
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Re: [Freesurfer] How to extract cortical features of a ROI

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

you can use mri_segstats with the --slabel option

On 3/5/19 10:35 AM, Bruce Fischl wrote:
> Hi Kan
>
> you can give the surface-based label to mris_anatomical_stats and it 
> will constrain it's calculations to the label (where it makes sense):
>
> mris_anatomical_stats -l  ...
>
> you can probably do it with mri_segstats too - Doug will know
>
> cheers
> Bruce
>
>
> On Tue, 5 Mar 2019, 310913949 wrote:
>
>>
>> External Email - Use Caution
>>
>> Hi bruce??
>>    I still have some questions about extracting cortical features of 
>> a ROI. I used the
>> mri_label2label to sample the volumetric label to the surface of the 
>> subject. But I dont know how to
>> do next, as i found that the RAS coordinates do  not correspond to 
>> the coordinates in the
>> lh.thickness, and why?
>>     Besides, I found the  web of how to extract cortical thickness 
>> values for a region-of-interest
>> (ROI) defined in volume
>> space(https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness).But
>>  
>> it doesn't report
>> the coordinates information. How can I get the ROI's coordinates 
>> information if i use this method?
>>     Thanks for your help!
>>     Kan Deng
>>
>>
>>
>> -- Original --
>> From:  "Bruce Fischl";
>> Date:  Fri, Jan 25, 2019 10:58 PM
>> To:  "Freesurfer support list";
>> Subject:  Re: [Freesurfer] How to extract cortical features of a ROI
>>
>> Hi Kan
>>
>> if you draw a volumetric label you first need to sample it to the 
>> surface
>> of that subject (mri_label2label --sample). If all you want are stats 
>> from
>> the subject there is no need to map it to fsaverage - that is only
>> necessary if you want to use a group coordinate system.
>>
>> cheers
>> Bruce
>>
>>
>>
>> On Fri, 25 Jan 2019,
>> 310913949 wrote:
>>
>> >
>> >  External Email - Use Caution
>> >
>> >
>> > Dear Freesurfer Experts,
>> >        I want to extract cortical features of a ROI that I drawn 
>> manually on  the rawavg.mgz in
>> Freesurfer, but i
>> > don't know how to do that. I think maybe first the  lesion mask 
>> should be registered to the
>>  standard templates
>> > fsaverage, but I don't know what the command line is , could  you 
>> tell me?  And secondly, I should
>> use
>> > mri_label2label to map the label to individual subject  and extract 
>> the cortical features of the
>> ROI, am I right?
>> >       I am looking forward to your reply!Thanks.
>> >
>> >                                                   Best wishes!
>> >                                                       Kan Deng
>> >
>> >
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>>
>>
>
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Re: [Freesurfer] Gray matter segmentation

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

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

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

What is actually in the gii file? It is expecting only to read in 
overlay information (eg, a binary mask with values of 0 or 1 at each 
vertex). I have not used gifti all that much

On 3/4/19 10:55 AM, CAGNA Bastien wrote:
>
> External Email - Use Caution
>
> Hi everyone,
> I need to convert a surfacic mask that is made from data of one 
> subject projected onto fsaverage6 into a volumic map. To do so, I'm 
> trying to use mri_surf2vol to take my Gifti file and create 3D version 
> as Nifti file (using gray matter). So, I tryed this:
> mri_surf2vol --sd [subjects_dir] --subject fsaverage6 --o 
> [output_filename].nii.gz --so [subjects_dir]/fsaverage6/surf/lh.white 
> [lh.surf_mask_filename].gii --so 
> [subjects_dir]/fsaverage6/surf/lh.white [rh.surf_mask_filename].gii
>
> But it failed and tells me:
> MRISreadGiftiAsMRI: no overlay data found in file 
> [lh.surf_mask_filename].gii
>
> After quickly looking to the source code, at line 1077 of utils/gifti.cpp:
> //*---
>   MRISreadGiftiAsMRI() - reads GIFTI functional frames into
>   an MRI volume struct, which is a retro-fit usage to store
>   multiple frames of data (where in this case, a frame is one
>   complete vector of vertices).
>   This routine will only read NIFTI_INTENT_TIME_SERIES data
>   arrays.
> ---*//
> I'm getting confused because (from what I understood) this function is 
> trying to read gifti's data in a nifti and moreover i didn't find any 
> example on the web of resampling Gifti file to Nifti image using 
> mri_surf2vol. I think I missing some think but do not understand what.
>
> Does any one have an idea about it?
>
> Best regards,
> Bastien CAGNA
>
>
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Re: [Freesurfer] Cerebellar Cortex Reconstruction

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

that mri_tessellate command should have worked. It might be a gifti 
problem. Can you run it with our standard surface as an output and view 
it in freeview?

On 3/3/19 11:47 AM, Max Crayen wrote:
>  External Email - Use Caution
>
> Hi Bruce,
>
> we are 3D printing brains in our lab, at the moment mainly for visualization 
> purposes.
> Of course, the most important parts are the cortex reconstructions of the 
> left and right hemispheres
> and we are very satisfied with the results.
>
> But we were also thinking about an entire brain model
> and so we looked for a way to reconstruct the cerebellum or even the 
> brainstem.
>
> Is there any way to create such reconstructions with freesurfer, even if they 
> are not so detailed or show defects?
>
>
> Best regards,
> Max
>
>> Gesendet: Sonntag, 03. März 2019 um 17:07 Uhr
>> Von: "Bruce Fischl" 
>> An: "Freesurfer support list" 
>> Betreff: Re: [Freesurfer] Cerebellar Cortex Reconstruction
>>
>> Hi Max
>>
>> we don't have a released version of a cerebellar reconstruction. We have
>> messed around with doing so, but the issue is that the folia are *so*
>> small, that at 1mm-ish resolution you miss a ton of them (and get
>> topological defects, etc...).
>>
>> As for the brainstem, we don't, but why would you want such a thing?
>> Surface models are usually only useful for laminar structures.
>>
>> cheers
>> Bruce
>>
>>
>> On Sat, 2 Mar 2019, Max Crayen wrote:
>>
>>>  External Email - Use Caution
>>>
>>> Dear all,
>>>   
>>> I ran recon-all with my dataset and I am pretty satisfied with the cortical 
>>> reconstruction of both
>>> hemispheres.
>>> Unfortnuately, there was no Cerebellar reconstrucion.
>>> Is there any way to also get a surface reconstruction of the cerebellum 
>>> with recon-all or is there
>>> even a seperate command for that?
>>>   
>>>   
>>> I tried to do it with
>>> mri_tessellate /mri/aseg.mgz 8 /lh_cerebellum.gii
>>> mri_tessellate /mri/aseg.mgz 47 /rh_cerebellum.gii
>>>   
>>> and also with
>>> mri_vol2surf --mov /mri/aseg.mgz --hemi lh --surf cerebellum --mni152reg  
>>> --o /lh_cerebellum.gii
>>> but both times the created .gii file seems to be empty.
>>>   
>>> I read myself through many Archive threads and the freesurfer wiki, but 
>>> since I am not using
>>> freesurfer regularly, I do not know what else I could do.
>>>   
>>> And if a surface reconstruction is possible for the cerebellum, is it also 
>>> possible for the brain
>>> stem?
>>>   
>>> Thanks alot in advance!
>>>   
>>> Best regards,
>>> Max Crayen
>>>
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Re: [Freesurfer] recon-all Workflow Help

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

Sorry Riya, you have to run it all.
doug

On 3/3/19 11:36 AM, Riya Chatterjee wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I am new to FreeSurfer - I am a high school sophomore trying to learn 
> more about processing brain MRI's. I have read through most of the 
> documentation, but I was not sure about the workflow for processing an 
> MRI. I am trying to extract just surfaces and was wondering if I can 
> run "recon-all -autorecon2 -pial..." without running "recon-all 
> -all...". Basically, I'm trying to see if I need to run the "recon-all 
> -all..." step before running any of the sub-processes. I would greatly 
> appreciate any advice I could get on this, thanks.
>
> Thanks,
> Riya C
>
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[Freesurfer] Gradient Inhomogeneity Correction in Bay3

[Chinappen, Dhinakaran Maheswaran]

Dear Freesurfer community,

We acquired images in Bay3 and would like to know where the gradient 
inhomogeneity correction files would be on cluster, if any.

We are familiar with the Bay4 procedure for correcting for inhomogeneity and 
were also wondering if similar steps would be followed for images acquired in 
Bay3.

Thank you!
Dhinakaran.

--

Dhinakaran M. Chinappen

Clinical Research Coordinator

Neurology Department

Massachusetts General Hospital

m: 1-267-257-1224
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Re: [Freesurfer] PETSurfer: Equivalence between surfaces un gtmseg space and native surface?

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

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

[Matthieu Vanhoutte]

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] mri_segstats issue with hippocampal subfields

[Bruce Fischl]

Hi Daniel

left and right hippocampus have different indices (17 and 53)

cheers
Bruce
On Wed, 6 Mar 
2019, Daniel Callow wrote:




External Email - Use Caution

Never mind. I see that I can use those to id #'s to call from 
FreeSurferColorLUT.txt.

I assume that those Id's are consistent for both left and right hippocampus.

Thanks for the help!
Daniel CallowPhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298


On Wed, Mar 6, 2019 at 1:09 PM Daniel Callow  wrote:
  Hi Doug,
Thank you for your reply!


Unfortunately when I run the same code as before but by calling
to /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 
instead
of /Applications/freesurfer/FreeSurferColorLUT.txt and using the assosciated 
--id #'s as shown below 

mri_segstats --seg 
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz --mul 
1000
--ctab 
/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt --id 
226 --id 205
--id 206 --id 208 --id 209 --id 210 --i
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./radialdiff-masked.nii.gz 
--sum
${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.radialdiff.stats



I get the following error.


Loading /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest./rhipp2diff.nii.gz

CTABreadASCII(/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt):
 badly
formed file

No such file or directory

ERROR: reading 
/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt


any idea how I could make it a formed file that is compatible?


Best,

Daniel CallowPhD Student, Neuroscience and Cognitive Science
Exercise for Brain Health Lab
University of Maryland, College Park
ddcc2...@gmail.com
443-254-6298


On Wed, Mar 6, 2019 at 12:56 PM Greve, Douglas N.,Ph.D. 
 wrote:
  look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt
  The first number should be the one you are looking for.

  On 3/6/19 12:26 PM, Daniel Callow wrote:
  >
  > External Email - Use Caution
  >
  > Hello,
  >
  > I am trying to extract stats from the hippocampal subfield volumes
  > that I have warped to diffusion space.
  >
  > mri_vol2vol --mov
  > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz
  > --targ
  
>/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz

  > --inv --interp nearest --o
  > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
  > --reg
  > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.dat
  > --no-save-reg
  >
  >
  > Then I run
  >
  >
  > mri_segstats --seg
  > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
  > --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --id 550 --id
  > 552 --id 556 --id 557 --id 558 --i
  > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./fa-masked.nii.gz
  > --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.fa.stats
  >
  >
  > using the --i id# from FreeSurferColorLUT.txt.
  >
  >
  > However, looking at the values of the hippocampal subfield volume I
  > see that the Id's are all in the 200's?
  >
  >
  > Is there a txt file that has the labelings like in
  > FreeSurferColorLUT.txt for these hippocampal subfields?
  >
  >
  > Thank you for any help you can provide!
  >
  > *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] extracting cortical parcellation

[Bruce Fischl]

Hi  Atena

the vertex indices are stored in the first column. You should be able to 
use them to look up into any overlay you want


cheers
Bruce


On Wed, 6 Mar 2019, Atena Rezaei wrote:



External Email - Use Caution

Hi Bruce,
I am going to extract the cortical parcellation file with its color table from 
freesurfer then import that
in the other interface to detect and visualize the somatosensory (3b broadmann 
) area. Therefore, I need
the fifth column with some values for vertices. 

BR,
Atena


On Wed, Mar 6, 2019 at 5:47 PM Bruce Fischl  wrote:
  Hi Atena

  what were you hoping would be in the fifth column? What are you hoping to
  create your own annotation files from? Can you give us a bigger picture of
  what you are trying to achieve?

  cheers
  Bruce


  On Wed, 6 Mar 2019, Atena Rezaei
  wrote:

  >
  > External Email - Use Caution
  >
  > Hi Bruce,
  >
  > Thanks for your comment!
  > I used mri_annotation2label to existed lh.aparc.annot file in label 
folder
  > and got the labels. but the labels' text file contain 0 in fifth column.
  > I need to create atlas from my own data  including surface 
parcellation. how
  > can I do that? I found commands;
  > mris_ca_train and mris_ca_label,
  > how can I make the annotation files from my own data?
  >
  > BR,
  > Atena
  >
  > On Wed, Mar 6, 2019 at 1:10 AM Bruce Fischl 
  > wrote:
  >       Hi Atena
  >
  >       yes, mri_annotation2label should work, although it really
  >       depends on what
  >       you want to do next
  >
  >       cheers
  >       Bruce
  >       On Wed, 6 Mar 2019, Atena Rezaei wrote:
  >
  >       >
  >       > External Email - Use Caution
  >       >
  >       > Hello,
  >       >
  >       > I am trying to extract the cortical parcellation(atlas) file
  >       from freesurfer with all the labels. I found
  >       > the lh.aparc.annot file in label folder. Should I use
  >       mri_annotation2label to create labels? or how can I
  >       > extract the whole file?
  >       > Thanks for ur help!
  >       >
  >       > BR,
  >       > Atena
  >       >
  >       >
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  >
  >
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[Freesurfer] (no subject)

[Jahan, Bushra]

Hello - I'm wondering how to generate a label in FreeSurfer from peak 
activation in a cluster? Is there a specific command?
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Re: [Freesurfer] projfrac question

[Nasiriavanaki, Zahra]

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.

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 

Re: [Freesurfer] unable to map surface to fsaverage4

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

This is a bug in mris_preproc. I have created a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc
Copy this to $FREESURFER_HOME/bin (after making a backup of the one that 
is there)
let us know if this works


On 3/2/19 8:57 AM, Chenfei YE wrote:
>
> External Email - Use Caution
>
> Hi,
>
> I'm following the process described in https://www.cloudneuro.org/ to 
> predict age based on cortical thickness of an individual brain.
> I cannot map surface to the fsaverage4 template by the 2nd command:
>
> recon-all -s subject.id -qcache -target fsaverage4
>
> The error was shown like
>
> mri_surf2surf: could not read su​rface
> ./test2/surf/lh.fsaverage4.sphere.reg
>
> No such file or directory
>
> I tried to change the 1st command like:
>
> recon-all -i input_image -s subject.id -all -target fsavearge4
>
> But still the same error.
>
> My FreeSurfer version is 6.0.0. Maybe that's why I cannot successfully 
> run the code in https://www.cloudneuro.org/. But is there any way to 
> solve this problem? Thank you.
>
> Chenfei
>
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Re: [Freesurfer] mri_segstats issue with hippocampal subfields

[Daniel Callow]

External Email - Use Caution

Never mind. I see that I can use those to id #'s to call
from FreeSurferColorLUT.txt.

I assume that those Id's are consistent for both left and right hippocampus.

Thanks for the help!
*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 Wed, Mar 6, 2019 at 1:09 PM Daniel Callow  wrote:

> Hi Doug,
>
> Thank you for your reply!
>
>
> Unfortunately when I run the same code as before but by calling to 
> /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
> instead of /Applications/freesurfer/FreeSurferColorLUT.txt and using the
> assosciated --id #'s as shown below
>
> mri_segstats --seg
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
> --mul 1000 --ctab
> /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
> --id 226 --id 205 --id 206 --id 208 --id 209 --id 210 --i
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./radialdiff-masked.nii.gz
> --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.radialdiff.stats
>
>
>
> I get the following error.
>
>
> Loading /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest./rhipp2diff.nii.gz
>
> CTABreadASCII(/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt):
> badly formed file
>
> No such file or directory
>
> ERROR: reading
> /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
>
>
> any idea how I could make it a formed file that is compatible?
>
>
> 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
>
>
> On Wed, Mar 6, 2019 at 12:56 PM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt
>> The first number should be the one you are looking for.
>>
>> On 3/6/19 12:26 PM, Daniel Callow wrote:
>> >
>> > External Email - Use Caution
>> >
>> > Hello,
>> >
>> > I am trying to extract stats from the hippocampal subfield volumes
>> > that I have warped to diffusion space.
>> >
>> > mri_vol2vol --mov
>> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz
>> > --targ
>> >
>> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz
>>
>> > --inv --interp nearest --o
>> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
>> > --reg
>> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.dat
>> > --no-save-reg
>> >
>> >
>> > Then I run
>> >
>> >
>> > mri_segstats --seg
>> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
>> > --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --id 550 --id
>> > 552 --id 556 --id 557 --id 558 --i
>> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./fa-masked.nii.gz
>> > --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.fa.stats
>> >
>> >
>> > using the --i id# from FreeSurferColorLUT.txt.
>> >
>> >
>> > However, looking at the values of the hippocampal subfield volume I
>> > see that the Id's are all in the 200's?
>> >
>> >
>> > Is there a txt file that has the labelings like in
>> > FreeSurferColorLUT.txt for these hippocampal subfields?
>> >
>> >
>> > Thank you for any help you can provide!
>> >
>> > *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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>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] extracting cortical parcellation

[Atena Rezaei]

External Email - Use Caution

Hi Bruce,

I am going to extract the cortical parcellation file with its color table
from freesurfer then import that in the other interface to detect and
visualize the somatosensory (3b broadmann ) area. Therefore, I need the
fifth column with some values for vertices.

BR,
Atena


On Wed, Mar 6, 2019 at 5:47 PM Bruce Fischl 
wrote:

> Hi Atena
>
> what were you hoping would be in the fifth column? What are you hoping to
> create your own annotation files from? Can you give us a bigger picture of
> what you are trying to achieve?
>
> cheers
> Bruce
>
>
> On Wed, 6 Mar 2019, Atena Rezaei
> wrote:
>
> >
> > External Email - Use Caution
> >
> > Hi Bruce,
> >
> > Thanks for your comment!
> > I used mri_annotation2label to existed lh.aparc.annot file in label
> folder
> > and got the labels. but the labels' text file contain 0 in fifth column.
> > I need to create atlas from my own data  including surface parcellation.
> how
> > can I do that? I found commands;
> > mris_ca_train and mris_ca_label,
> > how can I make the annotation files from my own data?
> >
> > BR,
> > Atena
> >
> > On Wed, Mar 6, 2019 at 1:10 AM Bruce Fischl 
> > wrote:
> >   Hi Atena
> >
> >   yes, mri_annotation2label should work, although it really
> >   depends on what
> >   you want to do next
> >
> >   cheers
> >   Bruce
> >   On Wed, 6 Mar 2019, Atena Rezaei wrote:
> >
> >   >
> >   > External Email - Use Caution
> >   >
> >   > Hello,
> >   >
> >   > I am trying to extract the cortical parcellation(atlas) file
> >   from freesurfer with all the labels. I found
> >   > the lh.aparc.annot file in label folder. Should I use
> >   mri_annotation2label to create labels? or how can I
> >   > extract the whole file?
> >   > Thanks for ur help!
> >   >
> >   > BR,
> >   > Atena
> >   >
> >   >
> >   >___
> >   Freesurfer mailing list
> >   Freesurfer@nmr.mgh.harvard.edu
> >   https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
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Re: [Freesurfer] mri_segstats issue with hippocampal subfields

[Daniel Callow]

External Email - Use Caution

Hi Doug,

Thank you for your reply!


Unfortunately when I run the same code as before but by calling to
/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
instead of /Applications/freesurfer/FreeSurferColorLUT.txt and using the
assosciated --id #'s as shown below

mri_segstats --seg
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
--mul 1000 --ctab
/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt
--id 226 --id 205 --id 206 --id 208 --id 209 --id 210 --i
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./radialdiff-masked.nii.gz
--sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.radialdiff.stats



I get the following error.


Loading /Volumes/DANIEL/dti_freesurf/dtrecon/AES139.Rest./rhipp2diff.nii.gz

CTABreadASCII(/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt):
badly formed file

No such file or directory

ERROR: reading
/Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt


any idea how I could make it a formed file that is compatible?


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


On Wed, Mar 6, 2019 at 12:56 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt
> The first number should be the one you are looking for.
>
> On 3/6/19 12:26 PM, Daniel Callow wrote:
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> > I am trying to extract stats from the hippocampal subfield volumes
> > that I have warped to diffusion space.
> >
> > mri_vol2vol --mov
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz
> > --targ
> >
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz
>
> > --inv --interp nearest --o
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
> > --reg
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.dat
> > --no-save-reg
> >
> >
> > Then I run
> >
> >
> > mri_segstats --seg
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
> > --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --id 550 --id
> > 552 --id 556 --id 557 --id 558 --i
> > /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./fa-masked.nii.gz
> > --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.fa.stats
> >
> >
> > using the --i id# from FreeSurferColorLUT.txt.
> >
> >
> > However, looking at the values of the hippocampal subfield volume I
> > see that the Id's are all in the 200's?
> >
> >
> > Is there a txt file that has the labelings like in
> > FreeSurferColorLUT.txt for these hippocampal subfields?
> >
> >
> > Thank you for any help you can provide!
> >
> > *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] mri_segstats issue with hippocampal subfields

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

look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt
The first number should be the one you are looking for.

On 3/6/19 12:26 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> I am trying to extract stats from the hippocampal subfield volumes 
> that I have warped to diffusion space.
>
> mri_vol2vol --mov 
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz 
> --targ 
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz
>  
> --inv --interp nearest --o 
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz 
> --reg 
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.dat 
> --no-save-reg
>
>
> Then I run
>
>
> mri_segstats --seg 
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz 
> --ctab /Applications/freesurfer/FreeSurferColorLUT.txt --id 550 --id 
> 552 --id 556 --id 557 --id 558 --i 
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./fa-masked.nii.gz 
> --sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.fa.stats
>
>
> using the --i id# from FreeSurferColorLUT.txt.
>
>
> However, looking at the values of the hippocampal subfield volume I 
> see that the Id's are all in the 200's?
>
>
> Is there a txt file that has the labelings like in 
> FreeSurferColorLUT.txt for these hippocampal subfields?
>
>
> Thank you for any help you can provide!
>
> *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] Whitening/weighting matrix in FSFAST

[Zhi Li]

External Email - Use Caution

Thank you very much. I would like to whiten the data. May I know the
details of the whitening process used in FSFAST? If I could get the
whitening matrix (maybe from the source codes)?

Best regards,

Lizhi

On Wed, 6 Mar 2019 at 11:54, Greve, Douglas N.,Ph.D. 
wrote:

> Whitening is done by default (you can turn it off with -nowhiten to
> mkanalysis-sess). It uses an AR1 model.
>
> On 3/4/19 12:46 PM, Zhi Li wrote:
> >
> > External Email - Use Caution
> >
> > Hello Freesurfer Experts,
> >
> > May I ask if there is a whitening/weighting matrix used to give
> > weighted least squares estimates (WLS) and whiten the data during the
> > 1st-level model estimation in FSFAST? If so, how could I get it?
> >
> > Many thanks and kind regards,
> >
> > Lizhi
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
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[Freesurfer] mri_segstats issue with hippocampal subfields

[Daniel Callow]

External Email - Use Caution

Hello,

I am trying to extract stats from the hippocampal subfield volumes that I
have warped to diffusion space.

mri_vol2vol --mov
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz
--inv --interp nearest --o
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
--reg /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./register.dat
--no-save-reg


Then I run


mri_segstats --seg
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lhipp2diff.nii.gz
--ctab /Applications/freesurfer/FreeSurferColorLUT.txt --id 550 --id 552
--id 556 --id 557 --id 558 --i
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./fa-masked.nii.gz
--sum ${SUBJECTS_DIR}/${subj}.${cond}./stats/lhipp.fa.stats


using the --i id# from FreeSurferColorLUT.txt.


However, looking at the values of the hippocampal subfield volume I see
that the Id's are all in the 200's?


Is there a txt file that has the labelings like in FreeSurferColorLUT.txt
for these hippocampal subfields?


Thank you for any help you can provide!
*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] Group analysis

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

On 3/4/19 10:11 AM, Hengameh Marzbani wrote:
>
> External Email - Use Caution
>
> Hi Freesurfers,
>
> I want to do group analysis on four groups and use the volume values 
> in aseg,stats.
> 1- Is it correct that each subcortical segmentation is based on a 
> "volumetric segmentation atlas" created by Freesurfer?
Yes
> 2- Are the volume values expressed in the space of this atlas?
No, they are in native space units.
> 3- Can I compare these absolute values between 4 groups ?
Yes.
> 4- Should I apply correction to the volume measures by eTIV (also 
> called ICV)?
Probably so, but you should know better than us
>
>
> Thanks you in advance!
>
> Best regards,
> Hengameh
>
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Re: [Freesurfer] Whitening/weighting matrix in FSFAST

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

Whitening is done by default (you can turn it off with -nowhiten to 
mkanalysis-sess). It uses an AR1 model.

On 3/4/19 12:46 PM, Zhi Li wrote:
>
> External Email - Use Caution
>
> Hello Freesurfer Experts,
>
> May I ask if there is a whitening/weighting matrix used to give 
> weighted least squares estimates (WLS) and whiten the data during the 
> 1st-level model estimation in FSFAST? If so, how could I get it?
>
> Many thanks and kind regards,
>
> Lizhi
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] citing freesurfer

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

There was not freesurfer specific publication from dt_recon. It is 
really basic, so any publication that talks about fitting tensors to the 
diffusion data will do.

On 3/4/19 12:30 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello,
>
> How should I go about properly citing freesurfer if I am using 
> dt_recon for dti analysis?
>
> 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] Choroid plexus analysis

[Alan Francis]

External Email - Use Caution

Hi Ben -

Although I have not worked on this myself, it is my belief that FS
quantifies the CP fairly accurately.  The volumes of the CP are being used
in understanding etiology and pathogenesis of psychiatric disorders such as
Schizophrenia. The lab I worked in previously has someone working on this.

best,

Alan

On Tue, Feb 19, 2019 at 7:27 AM Benjamin Luerweg <
luer...@students.uni-marburg.de> wrote:

> External Email - Use Caution
>
> Dear community,
>
> anyone out there who can give me some information regarding how valid a
> volume detection of the choroid plexus is?
> I used fs 6.0.
>
> Kind regards,
> Ben
>
>
>
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-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*




*Alan N. Francis PhDInstructor in PsychiatryHarvard Medical School*



*Louis V. Gerstner III scholarMartinos Center for Biomedical Imaging*

*Massachusetts General Hospital*

*149, 13th street, Charlestown, MA*

*al...@bwh.harvard.edu  *
*afran...@mclean.harvard.edu *
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Re: [Freesurfer] extracting cortical parcellation

[Bruce Fischl]

Hi Atena

what were you hoping would be in the fifth column? What are you hoping to 
create your own annotation files from? Can you give us a bigger picture of 
what you are trying to achieve?


cheers
Bruce


On Wed, 6 Mar 2019, Atena Rezaei 
wrote:




External Email - Use Caution

Hi Bruce,

Thanks for your comment!
I used mri_annotation2label to existed lh.aparc.annot file in label folder
and got the labels. but the labels' text file contain 0 in fifth column.
I need to create atlas from my own data  including surface parcellation. how
can I do that? I found commands;
mris_ca_train and mris_ca_label,
how can I make the annotation files from my own data?

BR,
Atena

On Wed, Mar 6, 2019 at 1:10 AM Bruce Fischl 
wrote:
  Hi Atena

  yes, mri_annotation2label should work, although it really
  depends on what
  you want to do next

  cheers
  Bruce
  On Wed, 6 Mar 2019, Atena Rezaei wrote:

  >
  > External Email - Use Caution
  >
  > Hello,
  >
  > I am trying to extract the cortical parcellation(atlas) file
  from freesurfer with all the labels. I found
  > the lh.aparc.annot file in label folder. Should I use
  mri_annotation2label to create labels? or how can I
  > extract the whole file?
  > Thanks for ur help!
  >
  > BR,
  > Atena
  >
  >
  >___
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[Freesurfer] curved reformat image....

[Gonzalo Rojas Costa]

External Email - Use Caution

Hi:

  How can I get in an automatic way curved reformat images (for
example, see paper
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009174/)

  Sincerely,


Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl
http://www.aribrain.info
https://scholar.google.com/citations?user=LO7LZ3oJ
https://www.researchgate.net/profile/Gonzalo_Rojas2
https://cl.linkedin.com/in/gonzalorojascosta

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Re: [Freesurfer] extracting cortical parcellation

[Atena Rezaei]

External Email - Use Caution

Hi Bruce,

Thanks for your comment!
I used mri_annotation2label to existed lh.aparc.annot file in label folder
and got the labels. but the labels' text file contain 0 in fifth column.
I need to create atlas from my own data  including surface parcellation.
how can I do that? I found commands;
mris_ca_train and mris_ca_label,
how can I make the annotation files from my own data?

BR,
Atena

On Wed, Mar 6, 2019 at 1:10 AM Bruce Fischl 
wrote:

> Hi Atena
>
> yes, mri_annotation2label should work, although it really depends on what
> you want to do next
>
> cheers
> Bruce
> On Wed, 6 Mar 2019, Atena Rezaei wrote:
>
> >
> > External Email - Use Caution
> >
> > Hello,
> >
> > I am trying to extract the cortical parcellation(atlas) file from
> freesurfer with all the labels. I found
> > the lh.aparc.annot file in label folder. Should I use
> mri_annotation2label to create labels? or how can I
> > extract the whole file?
> > Thanks for ur help!
> >
> > BR,
> > Atena
> >
> >
> >___
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Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

[Bruce Fischl]

are they currently labeled 0? Where did you get your color LUT from?
On Wed, 
6 Mar 2019, Jörg Stadler wrote:



   External Email - Use Caution

Hi Bruce,
this did not change anything. But I tried the process of mris_ca_train,
mris_ca_label with lh.oasis.chubs.annot and this worked fine.

A closer look to my source annot file from mris_seg2annot showed that
the label 'unknown' is missing.

How can I add the unknown to all unlabeled vertices?

cheers,
Joerg




Hi Joerg

I'm not positive that I understand, but have you tried giving
mris_ca_label the switch:

mris_ca_label -l $SUBJECTS_DIR/$subject/label/$hemi.cortex.label ...


that should remove non-cortical regions from your output annot

cheers
Bruce

On Tue, 5 Mar 2019, Jörg Stadler wrote:


   External Email - Use Caution
Hi,

I transfered the SPM Anatomy Toolbox
(http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMAnatomyToolbox_node.html)

from Collin space to fsaverage using

Wu J, Ngo GH, Greve DN, Li J, He T, Fischl B, Eickhoff SB, Yeo BTT.
*Accurate nonlinear mapping between MNI volumetric and FreeSurfer
surface coordinate systems*
,

/Human Brain Mapping/ 39:3793–3808, 2018.


mris_seg2annot --seg rh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s
fsaverage --hemi rh --o rh.anat_v22c

mris_seg2annot --seg lh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s
fsaverage --hemi lh --o lh.anat_v22c


This gave me the annot files for fsaverage (annotation.png) and a
template for the color lookup table.


Training of the classifier:

mris_ca_train -t Anatomy_v22c_LUT.txt lh lh.sphere.reg anat_v22c.annot
fsaverage lh.Anatomy_v22c.gcs

mris_ca_train -t Anatomy_v22c_LUT.txt rh rh.sphere.reg anat_v22c.annot
fsaverage rh.Anatomy_v22c.gcs


Transfer to individual subject fsaverage:

mris_ca_label fs_average lh sphere.reg lh.Anatomy_v22c.gcs
Anatomy_v22c.annot
mris_ca_label fs_average rh sphere.reg rh.Anatomy_v22c.gcs
Anatomy_v22c.annot


Now the miracle occurred and the whole surface got labeled.
(mris_ca_label.png)

How can a keep unassigned regions unlabeled?


Joerg


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[Freesurfer] DPABISurf: A Surface-Based Resting-State fMRI Data Analysis Toolbox

[YAN Chao-Gan]

External Email - Use Caution

Dear Colleagues,

We are pleased to announce the release of DPABISurf! DPABISurf is a
surface-based resting-state fMRI data analysis toolbox evolved from
DPABI/DPARSF, as easy-to-use as DPABI/DPARSF. DPABISurf is based on
fMRIPprep 1.3.0.post3 (Esteban et al., 2018)(RRID:SCR_016216), and based on
FreeSurfer 6.0.1 (Dale et al., 1999)(RRID:SCR_001847), ANTs 2.2.0 (Avants
et al., 2008)(RRID:SCR_004757), FSL 5.0.9 (Jenkinson et al.,
2002)(RRID:SCR_002823), AFNI 20160207 (Cox, 1996)(RRID:SCR_005927), SPM12
(Ashburner, 2012)(RRID:SCR_007037), PALM alpha112 (Winkler et al., 2016),
GNU Parallel (Tange, 2011), MATLAB (The MathWorks Inc., Natick, MA, US)
(RRID:SCR_001622), Docker (https://docker.com) (RRID:SCR_016445), and DPABI
V4.0 (Yan et al., 2016)(RRID:SCR_010501). DPABISurf provides user-friendly
graphical user interface (GUI) for pipeline surface-based preprocessing,
statistical analyses and results viewing, while requires no
programming/scripting skills from the users.



The DPABISurf pipeline first converts the user specified data into BIDS
format (Gorgolewski et al., 2016), and then calls fMRIPprep 1.3.0.post3
docker to preprocess the structural and functional MRI data, which
integrates FreeSurfer, ANTs, FSL and AFNI. With fMRIPprep, the data is
processed into FreeSurfer fsaverage5 surface space and MNI volume space.
DPABISurf further performs nuisance covariates regression (including
ICA-AROMA) on the surface-based data (volume-based data is processed as
well), and then calculate the commonly used R-fMRI metrics: amplitude of
low frequency fluctuation (ALFF) (Zang et al., 2007), fractional ALFF (Zou
et al., 2008), regional homogeneity (Zang et al., 2004), degree centrality
(Zuo and Xing, 2014), and seed-based functional connectivity. DPABISurf
also performs surface-based smoothing by calling FreeSurfer’s mri_surf2surf
command. These processed metrics then enters surfaced-based statistical
analyses within DPABISurf, which could perform surfaced-based permutation
test with TFCE by integrating PALM. Finally, the corrected results could be
viewed by the convenient surface viewer DPABISurf_VIEW, which is derived
from spm_mesh_render.m.



DPABISurf is designed to make surface-based data analysis require minimum
manual operations and almost no programming/scripting experience. We
anticipate this open-source toolbox will assist novices and expert users
alike and continue to support advancing R-fMRI methodology and its
application to clinical translational studies.

DPABISurf is open-source and distributed under GNU/GPL, available with
DPABI at http://www.rfmri.org/dpabi. It supports Windows 10 Pro, MacOS and
Linux operating systems. You can run it with or without MATLAB.

1. With MATLAB.

1.1. Please go to http://www.rfmri.org/dpabi to download DPABI.

1.2. Add with subfolders for DPABI in MATLAB's path setting.

1.3. Input 'dpabi' and then follow the instructions of the "Install" Button
on DPABISurf.


2. Without MATLAB.

2.1. Install Docker.

2.2. Terminal: docker pull cgyan/dpabi

2.3. Terminal: docker run -d --rm -v
/My/FreeSurferLicense/Path/license.txt:/opt/freesurfer/license.txt
-v /My/Data/Path:/data -p 5925:5925 cgyan/dpabi x11vnc -forever -shared
-usepw -create -rfbport 5925 &

/My/FreeSurferLicense/Path/license.txt: Where you stored the
FreeSurferLicense got from
https://surfer.nmr.mgh.harvard.edu/registration.html.

/My/Data/Path: This is where you stored your data. In Docker, the path is
/data.

2.4. Open VNC Viewer, connect to localhost:5925, the password is 'dpabi'.

2.5. In the terminal within the VNC Viewer, input "bash", and then input:

/opt/DPABI/DPABI_StandAlone/run_DPABI_StandAlone.sh ${MCRPath}

Now please enjoy the StandAlone version of DPABISurf with GUI!


References:

   - Ashburner, J. (2012). SPM: a history. *Neuroimage*, 62(2), 791-800,
   doi:10.1016/j.neuroimage.2011.10.025.
   - Avants, B.B., Epstein, C.L., Grossman, M., Gee, J.C. (2008). Symmetric
   diffeomorphic image registration with cross-correlation: evaluating
   automated labeling of elderly and neurodegenerative brain. *Med Image
   Anal*, 12(1), 26-41, doi:10.1016/j.media.2007.06.004.
   - Cox, R.W. (1996). AFNI: software for analysis and visualization of
   functional magnetic resonance neuroimages. *Comput Biomed Res*, 29(3),
   162-173.
   - Dale, A.M., Fischl, B., Sereno, M.I. (1999). Cortical surface-based
   analysis. I. Segmentation and surface reconstruction. *Neuroimage*,
   9(2), 179-194, doi:10.1006/nimg.1998.0395.
   - Esteban, O., Markiewicz, C.J., Blair, R.W., Moodie, C.A., Isik, A.I.,
   Erramuzpe, A., Kent, J.D., Goncalves, M., DuPre, E., Snyder, M., Oya, H.,
   Ghosh, S.S., Wright, J., Durnez, J., Poldrack, R.A., Gorgolewski, K.J.
   (2018). fMRIPrep: a robust preprocessing pipeline for functional MRI. *Nat
   Methods*, doi:10.1038/s41592-018-0235-4.
   - Gorgolewski, K.J., Auer, T., Calhoun, V.D., 

[Freesurfer] GLM twin design

[Julian Macoveanu]

External Email - Use Caution

Dear FS List,

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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Re: [Freesurfer] mris_ca_label: assignment of emty surface to wrong label

[Jörg Stadler]

External Email - Use Caution

Got it :)


filling the unassigned vertices with 'unknown' using tksurfer solved my
problem.


cheers,

Joerg


> Hi Bruce,
> this did not change anything. But I tried the process of mris_ca_train,
> mris_ca_label with lh.oasis.chubs.annot and this worked fine.
>
> A closer look to my source annot file from mris_seg2annot showed that
> the label 'unknown' is missing.
>
> How can I add the unknown to all unlabeled vertices?
>
> cheers,
> Joerg
>
>
>
>> Hi Joerg
>>
>> I'm not positive that I understand, but have you tried giving
>> mris_ca_label the switch:
>>
>> mris_ca_label -l $SUBJECTS_DIR/$subject/label/$hemi.cortex.label ...
>>
>>
>> that should remove non-cortical regions from your output annot
>>
>> cheers
>> Bruce
>>
>> On Tue, 5 Mar 2019, Jörg Stadler wrote:
>>
>>>    External Email - Use Caution
>>> Hi,
>>>
>>> I transfered the SPM Anatomy Toolbox
>>> (http://www.fz-juelich.de/inm/inm-1/DE/Forschung/_docs/SPMAnatomyToolbox/SPMAnatomyToolbox_node.html)
>>>
>>> from Collin space to fsaverage using
>>>
>>> Wu J, Ngo GH, Greve DN, Li J, He T, Fischl B, Eickhoff SB, Yeo BTT.
>>> *Accurate nonlinear mapping between MNI volumetric and FreeSurfer
>>> surface coordinate systems*
>>> ,
>>>
>>> /Human Brain Mapping/ 39:3793–3808, 2018.
>>>
>>>
>>> mris_seg2annot --seg rh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s
>>> fsaverage --hemi rh --o rh.anat_v22c
>>>
>>> mris_seg2annot --seg lh_Anatomy_v22c.nii.gz --ctab-auto Anatomy_v22c --s
>>> fsaverage --hemi lh --o lh.anat_v22c
>>>
>>>
>>> This gave me the annot files for fsaverage (annotation.png) and a
>>> template for the color lookup table.
>>>
>>>
>>> Training of the classifier:
>>>
>>> mris_ca_train -t Anatomy_v22c_LUT.txt lh lh.sphere.reg anat_v22c.annot
>>> fsaverage lh.Anatomy_v22c.gcs
>>>
>>> mris_ca_train -t Anatomy_v22c_LUT.txt rh rh.sphere.reg anat_v22c.annot
>>> fsaverage rh.Anatomy_v22c.gcs
>>>
>>>
>>> Transfer to individual subject fsaverage:
>>>
>>> mris_ca_label fs_average lh sphere.reg lh.Anatomy_v22c.gcs
>>> Anatomy_v22c.annot
>>> mris_ca_label fs_average rh sphere.reg rh.Anatomy_v22c.gcs
>>> Anatomy_v22c.annot
>>>
>>>
>>> Now the miracle occurred and the whole surface got labeled.
>>> (mris_ca_label.png)
>>>
>>> How can a keep unassigned regions unlabeled?
>>>
>>>
>>> Joerg
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>

-- 
Dr. rer. nat. Joerg Stadler
Leibniz Institute for Neurobiology (LIN)
Special Lab Non-Invasive Brain Imaging
Brenneckestr. 6, D - 39118 Magdeburg
Tel.: +49-391-6263-92171 Fax: +49-391-6263-92589
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