date:20191212

Re: [Freesurfer] (no subject)

2019-12-12 Thread Boris Rauchmann

External Email - Use Caution

yes to both. I always get the error ERROR: cannot find aseg...

On Fri, Dec 13, 2019 at 12:58 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that
> folder?
>
> On 12/12/19 12:57 PM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg
> > BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> > SUBJECTS_DIR /Users/boris/Desktop/mydir
> > subject 1122
> > outvol aparc+BN_Atlas_subcotex.mgz
> > useribbon 0
> > baseoffset 0
> > RipUnknown 0
> >
> > Reading lh white surface
> >  /Users/boris/Desktop/mydir/1122/surf/lh.white
> >
> > Reading lh pial surface
> >  /Users/boris/Desktop/mydir/1122/surf/lh.pial
> >
> > Loading lh annotations from
> > /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
> > reading colortable from annotation file...
> > colortable with 36 entries read (originally
> >
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> >
> > Reading rh white surface
> >  /Users/boris/Desktop/mydir/1122/surf/rh.white
> >
> > Reading rh pial surface
> >  /Users/boris/Desktop/mydir/1122/surf/rh.pial
> >
> > Loading rh annotations from
> > /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
> > reading colortable from annotation file...
> > colortable with 36 entries read (originally
> >
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> > Have color table for lh white annotation
> > Have color table for rh white annotation
> > Loading ribbon segmentation from
> > /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
> >
> > Building hash of lh white
> >
> > Building hash of lh pial
> >
> > Building hash of rh white
> >
> > Building hash of rh pial
> > ERROR: cannot find aseg
> >
> >
> > I get the same result using aseg.mgz
> >
> > Thanks,
> > Boris
> >> Am 12.12.2019 um 17:37 schrieb Bruce Fischl
> >> mailto:fis...@nmr.mgh.harvard.edu>>:
> >>
> >> Hi Boris
> >>
> >> can you send us the full command line and screen output of the
> >> commands that are failing?
> >>
> >> cheers
> >> Bruce
> >> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
> >>
> >>> External Email - Use Caution
> >>> Thanks. unfortunately I get an error message when I use the --aseg
> >>> flag for BN_Atlas_subcotex.mgz but
> >>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
> >>> .../fs_all_subjects/xyz/mri/aseg.mgz
> >>> The file BN_Atlas_subcotex.mgz was created using:
> >>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
> >>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
> >>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
> >>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
> >>> Best,
> >>> Boris
> >>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D.
> >>> mailto:dgr...@mgh.harvard.edu>> wrote:
> >>>  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with
> >>> your
> >>>  subcortical ROIs added? If so, you can try merging it with the
> >>> aparc, eg,
> >>>
> >>>  mri_aparc2aseg --s subject --volmask --aseg
> >>> BN_Atlas_subcotex.mgz --o
> >>>  aparc+BN_Atlas_subcotex.mgz
> >>>
> >>>  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg,
> >>> and then
> >>>  run gtmseg as you have done below.
> >>>
> >>>  Let me know if that works
> >>>  doug
> >>>
> >>>  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
> >>>  >
> >>>  > External Email - Use Caution
> >>>  >
> >>>  > In this example tried it with only the subcortical
> >>> segmentations from
> >>>  > my atlas. Please find the logfile attached. It gives me back:
> >>> "tissue
> >>>  > type is not set" but I set it to 2 in the LUT.txt
> >>>  >
> >>>  > In principle look the following commands right to you?
> >>>  >
> >>>  > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
> >>>  > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
> >>>  >
> >>>  > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
> >>>  > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
> >>>  >
> >>>  > Ideally I would have a gtmseg with both, the subcortical and the
> >>>  > cortical structures, but only the subcortical would also be
> >>> fine as
> >>>  > long as I can get  mri_gtmpvc running on it.
> >>>  >
> >>>  > Thanks,
> >>>  > Boris
> >>>  >
> >>>  > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
> >>>  > mailto:dgr...@mgh.harvard.edu>
> >>> > wrote:
> >>>  >
> >>>  > Can you send the log file for each of the gtmseg runs?
> >>>  >
> >>>  > On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
> >>>  >>
> >>>  >> External Email - Use Caution
> >>>  >>
> >>>  >> Thank you! I have a gca for subcortical  and two gcs
> >>> (lh/rh) for
> >>>  >>

Re: [Freesurfer] Study specific template

2019-12-12 Thread Greve, Douglas N.,Ph.D.

When you say that you looked at the labels/segmentations and that 
nothing looked horribly wrong, would that mean that the labels are 
accurate and that they are not really outliers?

On 12/5/19 7:26 PM, Joshi, Nandita wrote:
>  External Email - Use Caution
>
> Hi Dr. Greve,
>
> Thanks so much for your response. The primary reason for my wanting to do 
> this is due to a large number of outliers in terms of area and volume. Our 
> subject population is cognitively impaired older adults > 60 yrs. The custom 
> surface based template might help in investigating the area outliers, but it 
> wouldn't help in investigating the volume outliers. Since the DK atlas is 
> constructed from a population 18-86 years including 10 people with 
> Alzheimer's Disease, I am not even sure if making a new volume atlas would 
> help.
>
> Attached are graphs showing the distribution of the region wise area, volume, 
> and thickness of all subjects in lh (filled circles) and rh (open circles). I 
> looked into the aparc and aseg labels in specific regions for the subjects 
> that are outliers, but nothing seems to have gone horribly wrong in terms of 
> parcellation. Any pointers on how I can investigate and if a custom volume 
> template might help?
>
> Thanks,
> Nandita
>   
>   
>
> On 12/5/19, 1:36 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Greve, Douglas N.,Ph.D."  dgr...@mgh.harvard.edu> wrote:
>
>  We currently do not have a mac build of mri_aparc2aseg, and we recommend
>  downloading the freesurfer dev release to resolve this issue.
>  
>  
>  
>  On 12/5/19 1:00 PM, Joshi, Nandita wrote:
>  >  External Email - Use Caution
>  >
>  > Thank you so much for that! The README file instructs to download 
> make_average_subject and platform specific mri_aparc2aseg. However, the mac 
> version of mri_aparc2aseg is missing in the patch. Could it be possible to 
> download it from elsewhere?
>  >
>  > - Nandita
>  >
>  >
>  >
>  > On 12/5/19, 12:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on 
> behalf of Greve, Douglas N.,Ph.D."  behalf of dgr...@mgh.harvard.edu> wrote:
>  >
>  >  USE CAUTION: External Message.
>  >
>  >  See the REAME file here
>  >  
> https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_pub_dist_freesurfer_6.0.0-2Dpatch_=DwIGaQ=shNJtf5dKgNcPZ6Yh64b-A=Bk3PG21nu20V-TX_S982zJE-KkrgCuPol41Dhbe_0mI=HRcVNlmwdK9YHH6teQ4oW9oc6SDFzz79TS63mOlbWIY=6p4504imNdnEktx-WXKqAlxMvMCQ1EYnJW_deB2CAWI=
>  >
>  >
>  >  On 12/5/19 11:47 AM, Joshi, Nandita wrote:
>  >  >
>  >  > External Email - Use Caution
>  >  >
>  >  > Hello,
>  >  >
>  >  > I am trying to make a study specific template based on the
>  >  > instructions at:
>  >  > 
> https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_SurfaceRegAndTemplates=DwIGaQ=shNJtf5dKgNcPZ6Yh64b-A=Bk3PG21nu20V-TX_S982zJE-KkrgCuPol41Dhbe_0mI=HRcVNlmwdK9YHH6teQ4oW9oc6SDFzz79TS63mOlbWIY=LmIaVqBLyDekwkZsc46m3nOdn25B7E96m_UuRzDu3Ew=
>  >  >
>  >  > However, on running the first step:
>  >  >
>  >  > make_average_subject --out newtemplate --subjects subj1 subj2 
> subj3 ...
>  >  >
>  >  > I get an error while running the recon-all is trying to run the 
> aparc
>  >  > to aseg step:
>  >  >
>  >  > #@# AParc-to-ASeg aparc Thu Dec5 11:29:33 EST 2019
>  >  >
>  >  > /Users/nandita/FreeSurfer_recon/newtemplate
>  >  >
>  >  > \n mri_aparc2aseg --s newtemplate --volmask --aseg 
> aseg.presurf.hypos
>  >  > --relabel mri/norm.mgz mri/transforms/talairach.m3z
>  >  > /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca
>  >  > mri/aseg.auto_noCCseg.label_intensities.txt \n
>  >  >
>  >  > relabeling unlikely voxels interior to white matter surface:
>  >  >
>  >  > norm: mri/norm.mgz
>  >  >
>  >  > XFORM: mri/transforms/talairach.m3z
>  >  >
>  >  > GCA: 
> /Applications/freesurfer/average/RB_all_2016-05-10.vc700.gca
>  >  >
>  >  > label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
>  >  >
>  >  > SUBJECTS_DIR /Users/nandita/FreeSurfer_recon
>  >  >
>  >  > subject newtemplate
>  >  >
>  >  > outvol 
> /Users/nandita/FreeSurfer_recon/newtemplate/mri/aparc+aseg.mgz
>  >  >
>  >  > useribbon 0
>  >  >
>  >  > baseoffset 0
>  >  >
>  >  > RipUnknown 0
>  >  >
>  >  > Reading lh white surface
>  >  >
>  >  > /Users/nandita/FreeSurfer_recon/newtemplate/surf/lh.white
>  >  >
>  >  > Reading lh pial surface
>  >  >
>  >  >

Re: [Freesurfer] (no subject)

2019-12-12 Thread Greve, Douglas N.,Ph.D.

Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that 
folder?

On 12/12/19 12:57 PM, Boris Rauchmann wrote:
>
> External Email - Use Caution
>
> My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
> BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
> SUBJECTS_DIR /Users/boris/Desktop/mydir
> subject 1122
> outvol aparc+BN_Atlas_subcotex.mgz
> useribbon 0
> baseoffset 0
> RipUnknown 0
>
> Reading lh white surface
>  /Users/boris/Desktop/mydir/1122/surf/lh.white
>
> Reading lh pial surface
>  /Users/boris/Desktop/mydir/1122/surf/lh.pial
>
> Loading lh annotations from 
> /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
>
> Reading rh white surface
>  /Users/boris/Desktop/mydir/1122/surf/rh.white
>
> Reading rh pial surface
>  /Users/boris/Desktop/mydir/1122/surf/rh.pial
>
> Loading rh annotations from 
> /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
> reading colortable from annotation file...
> colortable with 36 entries read (originally 
> /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
> Have color table for lh white annotation
> Have color table for rh white annotation
> Loading ribbon segmentation from 
> /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz
>
> Building hash of lh white
>
> Building hash of lh pial
>
> Building hash of rh white
>
> Building hash of rh pial
> ERROR: cannot find aseg
>
>
> I get the same result using aseg.mgz
>
> Thanks,
> Boris
>> Am 12.12.2019 um 17:37 schrieb Bruce Fischl 
>> mailto:fis...@nmr.mgh.harvard.edu>>:
>>
>> Hi Boris
>>
>> can you send us the full command line and screen output of the 
>> commands that are failing?
>>
>> cheers
>> Bruce
>> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
>>
>>> External Email - Use Caution
>>> Thanks. unfortunately I get an error message when I use the --aseg 
>>> flag for BN_Atlas_subcotex.mgz but
>>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
>>> .../fs_all_subjects/xyz/mri/aseg.mgz
>>> The file BN_Atlas_subcotex.mgz was created using:
>>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
>>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
>>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
>>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
>>> Best,
>>> Boris
>>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
>>> mailto:dgr...@mgh.harvard.edu>> wrote:
>>>  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with 
>>> your
>>>  subcortical ROIs added? If so, you can try merging it with the 
>>> aparc, eg,
>>>
>>>  mri_aparc2aseg --s subject --volmask --aseg 
>>> BN_Atlas_subcotex.mgz --o
>>>  aparc+BN_Atlas_subcotex.mgz
>>>
>>>  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, 
>>> and then
>>>  run gtmseg as you have done below.
>>>
>>>  Let me know if that works
>>>  doug
>>>
>>>  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
>>>  >
>>>  > External Email - Use Caution
>>>  >
>>>  > In this example tried it with only the subcortical 
>>> segmentations from
>>>  > my atlas. Please find the logfile attached. It gives me back: 
>>> "tissue
>>>  > type is not set" but I set it to 2 in the LUT.txt
>>>  >
>>>  > In principle look the following commands right to you?
>>>  >
>>>  > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
>>>  > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
>>>  >
>>>  > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
>>>  > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
>>>  >
>>>  > Ideally I would have a gtmseg with both, the subcortical and the
>>>  > cortical structures, but only the subcortical would also be 
>>> fine as
>>>  > long as I can get  mri_gtmpvc running on it.
>>>  >
>>>  > Thanks,
>>>  > Boris
>>>  >
>>>  > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
>>>  > mailto:dgr...@mgh.harvard.edu> 
>>> > wrote:
>>>  >
>>>  >     Can you send the log file for each of the gtmseg runs?
>>>  >
>>>  >     On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>>>  >>
>>>  >>     External Email - Use Caution
>>>  >>
>>>  >>     Thank you! I have a gca for subcortical  and two gcs 
>>> (lh/rh) for
>>>  >>     cortical structures.
>>>  >>     I created an annot (rh/lh) and a mgz using mris_ca_label
>>>  >>     and mri_ca_label for parcellation/segmentation stats.
>>>  >>
>>>  >>     For the PET analysis I have the following problem:
>>>  >>
>>>  >>     If I use this command: gtmseg --s test --o test.mgz --ctab
>>>  >>     /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz
>>>  >>     --ctx-annot BN_Atlas.annot --ctab 
>>>

Re: [Freesurfer] flat maps in native space

2019-12-12 Thread Greve, Douglas N.,Ph.D.

It is hard to say. The v6 hires stream does not work very well.

On 12/12/19 10:38 AM, Nasiriavanaki, Zahra wrote:
> Thanks a lot for your reply Doug.
> I will re-do my recon as you said.
> Do you think the "blurriness" might be because of inadequate inflating 
> of the surface? My expert option file was : mris_inflate -n 15 -w 10.
> In addition to your recommendations, do you think I need to increase "n"?
>
> Thanks
> Mona
>
> *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, December 11, 2019 7:04 PM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* Re: [Freesurfer] flat maps in native space
> I'm not sure what is going on here, but I would guess that the v6 hires
> stream is not behaving  very well. I would suggest using a patch I
> created the HCP. If you are in the version 6 environment, you can run
> recon-all.v6.hires the same way you did recon-all, but do not use -hires
> and instead use -conf2hires
>
> doug
>
>
> On 12/9/19 6:17 PM, Nasiriavanaki, Zahra wrote:
> > Dear Freesurfer experts
> >
> > Hi
> >
> > I have a follow up question regarding the flat maps in native space.
> > I was trying to re-do the "making cuts and flattening the maps" step,
> > but first I want to know if these individual maps looks ok to you.
> > As you see in some parts of the brain the suci and gyri are *blurred
> > *and this causes some of the cuts (the cut in Calcarine fissure) to be
> > distorted (image attached). I'm not sure if this is normal to see the
> > blurriness and distorted shape of the brain in individual maps or not.
> > Is it possible that reconstruction hasn't been done well and that's
> > causing this problem?
> >
> > Thanks a lot
> > Mona
> >
> >
> >
> >
> >
> > *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, November 8, 2019 12:19 PM
> > *To:* Bruce Fischl ; Freesurfer support
> > list 
> > *Subject:* Re: [Freesurfer] flat maps in native space
> > Hi Bruce
> >
> > Thanks for your reply.
> > Well, two of my subjects have this problem. I have two subjects with
> > correct flattened maps and for 3 other subjects "the mris_flatten"  is
> > still running.
> > I attached the directory and I would appreciate if you could please
> > take a look.
> >
> > Thanks
> > MOna
> >
> >
> > *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 Bruce Fischl
> > 
> > *Sent:* Friday, November 8, 2019 11:54 AM
> > *To:* Freesurfer support list 
> > *Subject:* Re: [Freesurfer] flat maps in native space
> > Hi Mona
> >
> > that is pretty strange looking. Is the data somewhere local that we can
> > take a look at it? I would guess that one of the cuts left a connection
> > around, but would need to look at it to tell. Have you flattened other
> > subjects successfully?
> >
> > cheers
> > Bruce
> >
> >
> > On Fri, 8 Nov 2019, Nasiriavanaki, Zahra
> > wrote:
> >
> > > Hi Freesurfer experts
> > >
> > > I was trying to make flat maps for individual subjects, following
> > instruction
> > > in
> > 
> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch.
> > > For some of my subjects, the flat maps are distorted (attached image).
> > > Please let me know what you think.
> > >
> > > Thanks
> > > Mona
> > >
> > > [IMAGE]
> > >
> > > Zahra (Mona) Nasiriavanaki
> > >
> > > Postdoctoral Research Fellow
> > >
> > > Martinos Center for Biomedical Imaging
> > >
> > > Massachusetts General Hospital
> > >
> > > 149 13th Street, 149-2615
> > >
> > > Charlestown, MA, USA, 02129
> > >
> > >
> > >
> > >
> > >
> >
> > ___
> > 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
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>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Group analysis with gray matter volume in FS 6.0

2019-12-12 Thread Greve, Douglas N.,Ph.D.

When you say "gray matter volume", does it mean you are trying to do a 
VBM-style analysis? You can't do VBM with FS. You can do an analysis of 
cortical GM volume in a similar way. When you run mris_preproc, specify 
"volume" as the --meas

On 12/12/19 12:58 PM, Marisa Cathryn Ross wrote:
>
> External Email - Use Caution
>
> Hello,
>
> Thanks in advance for your patience with what is probably a very basic 
> question!
>
> We would like to run a group analysis with gray matter volume at the 
> voxel level following manual edits, and we are unsure which .mgz file 
> is the proper output to use as the final output from manual edits. We 
> do not have brain.finalsurfs.manedit.mgz files. Which subject file is 
> the recommended output to use for a whole-brain voxel level group 
> analysis after manual edits? I have included a screenshot of an 
> example subject’s /mri directory below.
>
> A screenshot of text Description automatically generated
>
> Thank you,
>
> Marisa Ross
>
> -- 
>
> /Marisa C. Ross, MPA/
>
> PhD Candidate
>
>
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Re: [Freesurfer] flat maps in native space

2019-12-12 Thread Nasiriavanaki, Zahra

Hi

I was trying to run recon-all.v6.hires, but it doesn't give me permission. I am 
using a linux computer in Martinos center.
Could you please let me know how to solve it?

Thanks
Mona

[bee:Mona] (nmr-stable6-env) ./make_recon.sh osre_7T_all 009
./make_recon.sh: line 7: /usr/local/freesurfer/stable6/bin/recon-all.v6.hires: 
Permission denied


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: Thursday, December 12, 2019 10:38 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] flat maps in native space

Thanks a lot for your reply Doug.
I will re-do my recon as you said.
Do you think the "blurriness" might be because of inadequate inflating of the 
surface? My expert option file was : mris_inflate -n 15 -w 10.
In addition to your recommendations, do you think I need to increase "n"?

Thanks
Mona


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, December 11, 2019 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] flat maps in native space

I'm not sure what is going on here, but I would guess that the v6 hires
stream is not behaving  very well. I would suggest using a patch I
created the HCP. If you are in the version 6 environment, you can run
recon-all.v6.hires the same way you did recon-all, but do not use -hires
and instead use -conf2hires

doug


On 12/9/19 6:17 PM, Nasiriavanaki, Zahra wrote:
> Dear Freesurfer experts
>
> Hi
>
> I have a follow up question regarding the flat maps in native space.
> I was trying to re-do the "making cuts and flattening the maps" step,
> but first I want to know if these individual maps looks ok to you.
> As you see in some parts of the brain the suci and gyri are *blurred
> *and this causes some of the cuts (the cut in Calcarine fissure) to be
> distorted (image attached). I'm not sure if this is normal to see the
> blurriness and distorted shape of the brain in individual maps or not.
> Is it possible that reconstruction hasn't been done well and that's
> causing this problem?
>
> Thanks a lot
> Mona
>
>
>
>
>
> *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, November 8, 2019 12:19 PM
> *To:* Bruce Fischl ; Freesurfer support
> list 
> *Subject:* Re: [Freesurfer] flat maps in native space
> Hi Bruce
>
> Thanks for your reply.
> Well, two of my subjects have this problem. I have two subjects with
> correct flattened maps and for 3 other subjects "the mris_flatten"  is
> still running.
> I attached the directory and I would appreciate if you could please
> take a look.
>
> Thanks
> MOna
>
>
> *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 Bruce Fischl
> 
> *Sent:* Friday, November 8, 2019 11:54 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] flat maps in native space
> Hi Mona
>
> that is pretty strange looking. Is the data somewhere local that we can
> take a look at it? I would guess that one of the cuts left a connection
> around, but would need to look at it to tell. Have you flattened other
> subjects successfully?
>
> cheers
> Bruce
>
>
> On Fri, 8 Nov 2019, Nasiriavanaki, Zahra
> wrote:
>
> > Hi Freesurfer experts
> >
> > I was trying to make flat maps for individual subjects, following
> instruction
> > in
> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch.
> > For some of my subjects, the flat maps are distorted (attached image).
> > Please let me know what you think.
> >
> > Thanks
> > Mona
> >
> > [IMAGE]
> >
> > Zahra (Mona) Nasiriavanaki
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Center for Biomedical Imaging
> >
> > Massachusetts General Hospital
> >
> > 149 13th Street, 149-2615
> >
> > Charlestown, MA, USA, 02129
> >
> >
> >
> >
> >
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] (no subject)

2019-12-12 Thread Boris Rauchmann

External Email - Use Caution

My-Computer:~ boris$ mri_aparc2aseg --s 1122 --volmask --aseg 
BN_Atlas_subcotex.mgz --o aparc+BN_Atlas_subcotex.mgz
SUBJECTS_DIR /Users/boris/Desktop/mydir
subject 1122
outvol aparc+BN_Atlas_subcotex.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /Users/boris/Desktop/mydir/1122/surf/lh.white

Reading lh pial surface 
 /Users/boris/Desktop/mydir/1122/surf/lh.pial

Loading lh annotations from /Users/boris/Desktop/mydir/1122/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)

Reading rh white surface 
 /Users/boris/Desktop/mydir/1122/surf/rh.white

Reading rh pial surface 
 /Users/boris/Desktop/mydir/1122/surf/rh.pial

Loading rh annotations from /Users/boris/Desktop/mydir/1122/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from /Users/boris/Desktop/mydir/1122/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial
ERROR: cannot find aseg


I get the same result using aseg.mgz 

Thanks,
Boris
> Am 12.12.2019 um 17:37 schrieb Bruce Fischl :
> 
> Hi Boris
> 
> can you send us the full command line and screen output of the commands that 
> are failing?
> 
> cheers
> Bruce
> On Thu, 12 Dec 2019, Boris Rauchmann wrote:
> 
>> External Email - Use Caution
>> Thanks. unfortunately I get an error message when I use the --aseg flag for 
>> BN_Atlas_subcotex.mgz but
>> even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
>> .../fs_all_subjects/xyz/mri/aseg.mgz
>> The file BN_Atlas_subcotex.mgz was created using: 
>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
>> $SUBJECTS_DIR/BN_Atlas_subcortex.gca
>> $SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
>> Best,
>> Boris
>> On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
>>  wrote:
>>  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
>>  subcortical ROIs added? If so, you can try merging it with the aparc, 
>> eg,
>> 
>>  mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
>>  aparc+BN_Atlas_subcotex.mgz
>> 
>>  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then
>>  run gtmseg as you have done below.
>> 
>>  Let me know if that works
>>  doug
>> 
>>  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
>>  >
>>  > External Email - Use Caution
>>  >
>>  > In this example tried it with only the subcortical segmentations from
>>  > my atlas. Please find the logfile attached. It gives me back: "tissue
>>  > type is not set" but I set it to 2 in the LUT.txt
>>  >
>>  > In principle look the following commands right to you?
>>  >
>>  > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
>>  > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
>>  >
>>  > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
>>  > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
>>  >
>>  > Ideally I would have a gtmseg with both, the subcortical and the
>>  > cortical structures, but only the subcortical would also be fine as
>>  > long as I can get  mri_gtmpvc running on it.
>>  >
>>  > Thanks,
>>  > Boris
>>  >
>>  > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
>>  > mailto:dgr...@mgh.harvard.edu>> wrote:
>>  >
>>  > Can you send the log file for each of the gtmseg runs?
>>  >
>>  > On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
>>  >>
>>  >> External Email - Use Caution
>>  >>
>>  >> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for
>>  >> cortical structures.
>>  >> I created an annot (rh/lh) and a mgz using mris_ca_label
>>  >> and mri_ca_label for parcellation/segmentation stats.
>>  >>
>>  >> For the PET analysis I have the following problem:
>>  >>
>>  >> If I use this command: gtmseg --s test --o test.mgz --ctab
>>  >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz
>>  >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
>>  >>
>>  >> It gives me the right regions for subcortical structures but it
>>  >> looks like it uses the standard FS parcellation with my labels
>>  >> for the cortical parcellations (only 93 cortical regions instead
>>  >> of 210).
>>  >>
>>  >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz
>>  >> --ctx-annot

Re: [Freesurfer] "Bad CPU type in executable" error - Qdec

2019-12-12 Thread Hoopes, Andrew

Qdec, as well as tksurfer and tkmedit, are no longer supported on mac OS 10.15+ 
since they are 32-bit binaries. These programs are also no longer maintained in 
our development distribution, so you will have to use a different OS or move to 
a command line analysis.

Best
Andrew


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of 
leona.salew...@med.uni-duesseldorf.de 
Sent: Thursday, December 12, 2019 8:46 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] "Bad CPU type in executable" error - Qdec

External Email - Use Caution

Dear Ladies and Gentlemen,

I am trying to run „Qdec“ which worked pretty well until I installed the new 
version of macOS Catalina (version 10.15.1).
Since then, I always receive an error called "Bad CPU type in executable“. I am 
working with Freesurfer version 6.
Is there anything I can do about it?

Thank you for your support.

Yours sincerely

L. Salewski
Universitätsklinikum Düsseldorf
Germany

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Re: [Freesurfer] Creating intermediate surfaces between white and pial?

2019-12-12 Thread Tim Schäfer

External Email - Use Caution

Hi Bruce,

thanks, that's exactly what I was looking for!

Best,

Tim

> On December 12, 2019 at 5:39 PM Bruce Fischl  
> wrote:
> 
> 
> Hi Tim
> 
> mris_expand -thickness ...
> 
> should do the trick.  If you specify -thickness it will read in the 
> ?h.thickness file and interpret the  argument as a percentage of 
> thickness, which is what you want I think
> 
> cheers
> Bruce
> 
> 
> On Thu, 12 Dec 2019, Tim Schäfer wrote:
> 
> >External Email - Use Caution
> >
> > Dear FreeSurfer experts,
> >
> > I know that I can sample data from a certain depth between the white and 
> > pial surfaces, but is there any way to create an intermediate surface file 
> > (i.e., mesh)?
> >
> > I would like to create, e.g., a surface file that is at 10% of the distance 
> > between the white and pial surface.
> >
> > I had a look at mris_create_surface, but unless I misinterpreted the 
> > description of the command line arguments, it does not seem to be the 
> > proper tool for the job.
> >
> > Background: This is for visualization purposes. I would like to create a 
> > figure similar to Figure S1 from Bletsch et al. 2018 in tkmedit: 
> > https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fhbm.24230=hbm24230-sup-0002-suppinfo02.tiff
> >
> > Thanks for your time and all the best,
> >
> >
> > Tim
> >
> > --
> > Dr. Tim Schäfer
> > Postdoc Computational Neuroimaging
> > Department of Child and Adolescent Psychiatry, Psychosomatics and 
> > Psychotherapy
> > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >___
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-- 
Tim Schäfer

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Re: [Freesurfer] Creating intermediate surfaces between white and pial?

2019-12-12 Thread Bruce Fischl


Hi Tim

mris_expand -thickness ...

should do the trick.  If you specify -thickness it will read in the 
?h.thickness file and interpret the  argument as a percentage of 
thickness, which is what you want I think


cheers
Bruce


On Thu, 12 Dec 2019, Tim Schäfer wrote:


   External Email - Use Caution

Dear FreeSurfer experts,

I know that I can sample data from a certain depth between the white and pial 
surfaces, but is there any way to create an intermediate surface file (i.e., 
mesh)?

I would like to create, e.g., a surface file that is at 10% of the distance 
between the white and pial surface.

I had a look at mris_create_surface, but unless I misinterpreted the 
description of the command line arguments, it does not seem to be the proper 
tool for the job.

Background: This is for visualization purposes. I would like to create a figure 
similar to Figure S1 from Bletsch et al. 2018 in tkmedit: 
https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fhbm.24230=hbm24230-sup-0002-suppinfo02.tiff

Thanks for your time and all the best,


Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] (no subject)

2019-12-12 Thread Bruce Fischl


Hi Boris

can you send us the full command line and screen output of the commands 
that are failing?


cheers
Bruce
On Thu, 12 Dec 
2019, Boris Rauchmann wrote:




External Email - Use Caution

Thanks. unfortunately I get an error message when I use the --aseg flag for 
BN_Atlas_subcotex.mgz but
even, if I'm using the original aseg.mgz I get: ERROR: cannot find aseg
.../fs_all_subjects/xyz/mri/aseg.mgz

The file BN_Atlas_subcotex.mgz was created using: 
mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
$SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz
Best,
Boris

On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. 
 wrote:
  What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
  subcortical ROIs added? If so, you can try merging it with the aparc, eg,

  mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
  aparc+BN_Atlas_subcotex.mgz

  Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then
  run gtmseg as you have done below.

  Let me know if that works
  doug


  On 12/2/19 1:18 PM, Boris Rauchmann wrote:
  >
  > External Email - Use Caution
  >
  > In this example tried it with only the subcortical segmentations from
  > my atlas. Please find the logfile attached. It gives me back: "tissue
  > type is not set" but I set it to 2 in the LUT.txt
  >
  > In principle look the following commands right to you?
  >
  > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
  > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
  >
  > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
  > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
  >
  > Ideally I would have a gtmseg with both, the subcortical and the
  > cortical structures, but only the subcortical would also be fine as
  > long as I can get  mri_gtmpvc running on it.
  >
  > Thanks,
  > Boris
  >
  > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
  > mailto:dgr...@mgh.harvard.edu>> wrote:
  >
  >     Can you send the log file for each of the gtmseg runs?
  >
  >     On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
  >>
  >>     External Email - Use Caution
  >>
  >>     Thank you! I have a gca for subcortical  and two gcs (lh/rh) for
  >>     cortical structures.
  >>     I created an annot (rh/lh) and a mgz using mris_ca_label
  >>     and mri_ca_label for parcellation/segmentation stats.
  >>
  >>     For the PET analysis I have the following problem:
  >>
  >>     If I use this command: gtmseg --s test --o test.mgz --ctab
  >>     /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz
  >>     --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
  >>
  >>     It gives me the right regions for subcortical structures but it
  >>     looks like it uses the standard FS parcellation with my labels
  >>     for the cortical parcellations (only 93 cortical regions instead
  >>     of 210).
  >>
  >>     If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz
  >>     --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
  >>     --no-xcerseg I get all my 210 cortical parcellations but the
  >>     standard FS subcortical segmentations.
  >>
  >>     How can I use both in one gtmseg so that I can proceed with it
  >>     doing my PET analysis in PETSurfer? It is not totally clear for
  >>     me what to merge using xcerebralseg.
  >>
  >>     Thanks a lot!
  >>
  >>     On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D.
  >>     mailto:dgr...@mgh.harvard.edu>> wrote:
  >>
  >>         It gets the subcortical from apas+head.mgz which gets created
  >>         along the
  >>         way by xcerebralseg. You can create your own with
  >>         xcerebralseg by
  >>         specifying your volume as the mergevol. I think this will
  >>         work, but I'm
  >>         not sure. I'm assuming you've used the GCA to create your own
  >>         subcortical seg for the given subject
  >>
  >>         On 11/5/19 1:06 PM, Boris Rauchmann wrote:
  >>         >
  >>         > External Email - Use Caution
  >>         >
  >>         > I just realized that the above mentioned command (gtmseg
  >>         --s XYZ --o
  >>         > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
  >>         > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
  >>         --no-xcerseg)
  >>         > gives me only the cortical segmentation. Is there any way
  >>         to also
  >>         > include the subcortical segmentation based on my individual
  >>         atlas? I
  >>         > also have an

[Freesurfer] Creating intermediate surfaces between white and pial?

2019-12-12 Thread Tim Schäfer

External Email - Use Caution

Dear FreeSurfer experts,

I know that I can sample data from a certain depth between the white and pial 
surfaces, but is there any way to create an intermediate surface file (i.e., 
mesh)?

I would like to create, e.g., a surface file that is at 10% of the distance 
between the white and pial surface. 

I had a look at mris_create_surface, but unless I misinterpreted the 
description of the command line arguments, it does not seem to be the proper 
tool for the job.

Background: This is for visualization purposes. I would like to create a figure 
similar to Figure S1 from Bletsch et al. 2018 in tkmedit: 
https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fhbm.24230=hbm24230-sup-0002-suppinfo02.tiff

Thanks for your time and all the best,


Tim

--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] (no subject)

2019-12-12 Thread Boris Rauchmann

External Email - Use Caution

Thanks. unfortunately I get an error message when I use the --aseg flag for
BN_Atlas_subcotex.mgz but even, if I'm using the original aseg.mgz I get:
ERROR: cannot find aseg .../fs_all_subjects/xyz/mri/aseg.mgz

The file BN_Atlas_subcotex.mgz was created using:
mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz
$SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z
$SUBJECTS_DIR/BN_Atlas_subcortex.gca
$SUBJECTS_DIR/xyz/mri/BN_Atlas_subcotex.mgz

Best,
Boris

On Thu, Dec 12, 2019 at 12:30 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> What is in BN_Atlas_subcotex.mgz ? Is it like aseg.mgz but with your
> subcortical ROIs added? If so, you can try merging it with the aparc, eg,
>
> mri_aparc2aseg --s subject --volmask --aseg BN_Atlas_subcotex.mgz --o
> aparc+BN_Atlas_subcotex.mgz
>
> Then use aparc+BN_Atlas_subcotex.mgz as input to xcerebralseg, and then
> run gtmseg as you have done below.
>
> Let me know if that works
> doug
>
>
> On 12/2/19 1:18 PM, Boris Rauchmann wrote:
> >
> > External Email - Use Caution
> >
> > In this example tried it with only the subcortical segmentations from
> > my atlas. Please find the logfile attached. It gives me back: "tissue
> > type is not set" but I set it to 2 in the LUT.txt
> >
> > In principle look the following commands right to you?
> >
> > xcerebralseg --s 0120test --o apas+head+subcort_BN.mgz --m
> > BN_Atlas_subcotex.mgz --atlas BN_Atlas_subcortex.gca
> >
> > gtmseg --s 0120test --head apas+head+subcort_BN.mgz --ctab
> > subcort_BN_LUT.txt --o gtmseg+subcort_BN.mgz
> >
> > Ideally I would have a gtmseg with both, the subcortical and the
> > cortical structures, but only the subcortical would also be fine as
> > long as I can get  mri_gtmpvc running on it.
> >
> > Thanks,
> > Boris
> >
> > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>> wrote:
> >
> > Can you send the log file for each of the gtmseg runs?
> >
> > On 11/26/2019 1:09 PM, Boris Rauchmann wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Thank you! I have a gca for subcortical  and two gcs (lh/rh) for
> >> cortical structures.
> >> I created an annot (rh/lh) and a mgz using mris_ca_label
> >> and mri_ca_label for parcellation/segmentation stats.
> >>
> >> For the PET analysis I have the following problem:
> >>
> >> If I use this command: gtmseg --s test --o test.mgz --ctab
> >> /xyz/BN_Atlas_246_LUT.txt --head BN_Atlas_subcotex.mgz
> >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
> >>
> >> It gives me the right regions for subcortical structures but it
> >> looks like it uses the standard FS parcellation with my labels
> >> for the cortical parcellations (only 93 cortical regions instead
> >> of 210).
> >>
> >> If I use gtmseg --s 0059test --o onlyhead.gtmseg_test.mgz
> >> --ctx-annot BN_Atlas.annot --ctab '/xyz/BN_Atlas_246_LUT.txt'
> >> --no-xcerseg I get all my 210 cortical parcellations but the
> >> standard FS subcortical segmentations.
> >>
> >> How can I use both in one gtmseg so that I can proceed with it
> >> doing my PET analysis in PETSurfer? It is not totally clear for
> >> me what to merge using xcerebralseg.
> >>
> >> Thanks a lot!
> >>
> >> On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D.
> >> mailto:dgr...@mgh.harvard.edu>> wrote:
> >>
> >> It gets the subcortical from apas+head.mgz which gets created
> >> along the
> >> way by xcerebralseg. You can create your own with
> >> xcerebralseg by
> >> specifying your volume as the mergevol. I think this will
> >> work, but I'm
> >> not sure. I'm assuming you've used the GCA to create your own
> >> subcortical seg for the given subject
> >>
> >> On 11/5/19 1:06 PM, Boris Rauchmann wrote:
> >> >
> >> > External Email - Use Caution
> >> >
> >> > I just realized that the above mentioned command (gtmseg
> >> --s XYZ --o
> >> > BN.gtmseg.mgz --ctx-annot BN_Atlas.annot --ctab
> >> > '/media/XYZ/BN_Atlas_freesurfer/BN_Atlas_246_LUT.txt'
> >> --no-xcerseg)
> >> > gives me only the cortical segmentation. Is there any way
> >> to also
> >> > include the subcortical segmentation based on my individual
> >> atlas? I
> >> > also have an Atlas_subcortex.gca file available.
> >> >
> >> > Best,
> >> > Boris
> >> >
> >> > On Tue, Aug 13, 2019 at 5:10 PM Greve, Douglas N.,Ph.D.
> >> > mailto:dgr...@mgh.harvard.edu>
> >>  >> >> wrote:
> >> >
> >> > There is no cut off for the minimum size. As it gets
> >> smaller, the PVC
> >> > noise amplification will become bigger (it also

Re: [Freesurfer] flat maps in native space

2019-12-12 Thread Nasiriavanaki, Zahra

Thanks a lot for your reply Doug.
I will re-do my recon as you said.
Do you think the "blurriness" might be because of inadequate inflating of the 
surface? My expert option file was : mris_inflate -n 15 -w 10.
In addition to your recommendations, do you think I need to increase "n"?

Thanks
Mona


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, December 11, 2019 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] flat maps in native space

I'm not sure what is going on here, but I would guess that the v6 hires
stream is not behaving  very well. I would suggest using a patch I
created the HCP. If you are in the version 6 environment, you can run
recon-all.v6.hires the same way you did recon-all, but do not use -hires
and instead use -conf2hires

doug


On 12/9/19 6:17 PM, Nasiriavanaki, Zahra wrote:
> Dear Freesurfer experts
>
> Hi
>
> I have a follow up question regarding the flat maps in native space.
> I was trying to re-do the "making cuts and flattening the maps" step,
> but first I want to know if these individual maps looks ok to you.
> As you see in some parts of the brain the suci and gyri are *blurred
> *and this causes some of the cuts (the cut in Calcarine fissure) to be
> distorted (image attached). I'm not sure if this is normal to see the
> blurriness and distorted shape of the brain in individual maps or not.
> Is it possible that reconstruction hasn't been done well and that's
> causing this problem?
>
> Thanks a lot
> Mona
>
>
>
>
>
> *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, November 8, 2019 12:19 PM
> *To:* Bruce Fischl ; Freesurfer support
> list 
> *Subject:* Re: [Freesurfer] flat maps in native space
> Hi Bruce
>
> Thanks for your reply.
> Well, two of my subjects have this problem. I have two subjects with
> correct flattened maps and for 3 other subjects "the mris_flatten"  is
> still running.
> I attached the directory and I would appreciate if you could please
> take a look.
>
> Thanks
> MOna
>
>
> *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 Bruce Fischl
> 
> *Sent:* Friday, November 8, 2019 11:54 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] flat maps in native space
> Hi Mona
>
> that is pretty strange looking. Is the data somewhere local that we can
> take a look at it? I would guess that one of the cuts left a connection
> around, but would need to look at it to tell. Have you flattened other
> subjects successfully?
>
> cheers
> Bruce
>
>
> On Fri, 8 Nov 2019, Nasiriavanaki, Zahra
> wrote:
>
> > Hi Freesurfer experts
> >
> > I was trying to make flat maps for individual subjects, following
> instruction
> > in
> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch.
> > For some of my subjects, the flat maps are distorted (attached image).
> > Please let me know what you think.
> >
> > Thanks
> > Mona
> >
> > [IMAGE]
> >
> > Zahra (Mona) Nasiriavanaki
> >
> > Postdoctoral Research Fellow
> >
> > Martinos Center for Biomedical Imaging
> >
> > Massachusetts General Hospital
> >
> > 149 13th Street, 149-2615
> >
> > Charlestown, MA, USA, 02129
> >
> >
> >
> >
> >
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] selxavg in native space vs fsaverage space

2019-12-12 Thread Nasiriavanaki, Zahra

Hi Doug

Thanks a lot for your reply.
what I mean by native space, is to register each subject's functional data on 
their own anatomical data.
yes, I was using --surf self in my preprocessing and mkanalysis, but since I 
was not using any smoothing, fwhm=0 in both native and fsaverage analysis, I 
thought the results should not differ.

Thanks
Mona


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, December 11, 2019 6:41 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] selxavg in native space vs fsaverage space

Hi Mona, not sure what you are trying to do. When you say "native"
space, do you mean native functional space or native anatmical space?
If you want to analyze the data on the native surface, you can use
--surf self when you run preproc-sess and mkanalysis-sess (instead of
specifying fsaverage) and analyze the session separately (which is
better if you are trying to do a longitudinal analysis).

it is hard to answer your other question about why there is a diff
between fsaverage and native space analyses without seeing what the
differences are and without knowing what the actual native space is.
They are different analyses, so they will not give exactly the same
results.

doug

On 12/11/19 11:30 AM, Nasiriavanaki, Zahra wrote:
> Dear Freesurfer experts
>
> Hi
>
> I was trying to do selxavg in native space for individual subjects
> which I have analyzed them in "fsaverage" space before.
> I have two sessions of functional data for each subject. In order to
> register them on one T1, I put the functional data from both sessions
> in one bold folder and registered all of them to one T1.
> The maps that I acquired from these analysis are slightly different
> from "fsaverage" maps.  In "fsaverage" analysis, I analyzed each
> session separately (selxavg) and then concatenated (isxconcat) the two
> sessions at the end. I believe it is not possible to do this in
> "native" space, since I have to register all the functional data to
> one T1, right?
> I need to know what is causing the differences in "native" and
> "fsaverage" maps?
> I appreciate if you could reply.
>
> Thanks a lot
> Mona
>
>
>
> *Zahra (Mona) Nasiriavanaki*
>
> Postdoctoral Research Fellow
>
> Martinos Center for Biomedical Imaging
>
> Massachusetts General Hospital
>
> 149 13th Street, 149-2615
>
> Charlestown, MA, USA, 02129
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] "Bad CPU type in executable" error - Qdec

2019-12-12 Thread Leona.Salewski

External Email - Use Caution

Dear Ladies and Gentlemen,

I am trying to run „Qdec“ which worked pretty well until I installed the new 
version of macOS Catalina (version 10.15.1).
Since then, I always receive an error called "Bad CPU type in executable“. I am 
working with Freesurfer version 6.
Is there anything I can do about it?

Thank you for your support.

Yours sincerely

L. Salewski
Universitätsklinikum Düsseldorf
Germany
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[Freesurfer] Pial surface does not follow the gray/csf boundary

2019-12-12 Thread Ardesch, D.J.

External Email - Use Caution

Dear FreeSurfers,

I’m trying to create surface reconstructions for some small monkey scans (about 
half the size of a rhesus macaque). The white surfaces look fine, but I can’t 
seem to get the pial surfaces to extend properly to the edge of the gray 
matter. Is there a way to ‘force’ the mris_make_surfaces command to place the 
pial surface along a certain voxel intensity or intensity gradient?

As I understand it, mris_make_surfaces takes the ?h.orig surface and extends it 
into the gray matter until it finds the gray matter/csf boundary. I’ve 
therefore tried to edit the brain.finalsurfs.mgz and brainmask.mgz volumes such 
that all white matter voxels have an intensity of 110 and all other brain 
voxels have an intensity of 80, and added some smoothing to create an intensity 
gradient, but this did not make a difference. The gray matter surface is still 
placed about 1/5th of the way between the gray/white boundary and the gray/csf 
boundary. Adding a T2 scan did not help either.

My setup is the following:

  *   FreeSurfer v6.0.0
  *   MacOS 10.14.6
  *   Running FreeSurfer with the -hires flag (voxel size is 0.25 mm isotropic)

With some manual editing I’ve been able to complete all pipeline steps until 
the surface reconstruction, except the topology fixing because it created large 
inaccuracies in the occipital lobe (including the topology fixing step did not 
solve the problem either).

Any help would be greatly appreciated!

With kind regards,
Dirk Jan

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Re: [Freesurfer] (no subject)

Re: [Freesurfer] Study specific template

Re: [Freesurfer] (no subject)

Re: [Freesurfer] flat maps in native space

Re: [Freesurfer] Group analysis with gray matter volume in FS 6.0

Re: [Freesurfer] flat maps in native space

Re: [Freesurfer] (no subject)

Re: [Freesurfer] "Bad CPU type in executable" error - Qdec

Re: [Freesurfer] Creating intermediate surfaces between white and pial?

Re: [Freesurfer] Creating intermediate surfaces between white and pial?

Re: [Freesurfer] (no subject)

[Freesurfer] Creating intermediate surfaces between white and pial?

Re: [Freesurfer] (no subject)

Re: [Freesurfer] flat maps in native space

Re: [Freesurfer] selxavg in native space vs fsaverage space

[Freesurfer] "Bad CPU type in executable" error - Qdec

[Freesurfer] Pial surface does not follow the gray/csf boundary

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