Can you upload the subject to our file drop system?

www.nmr.mgh.harvard.edu/facility/filedrop/index.html




On 06/04/2012 12:24 PM, Leon wrote:
> Hi, Douglas
>
> Thank you very much for the updated one. I tested the new codes and
> the problem is still there. The ID for the original version that
> generates a mask with one missing ROI is:
>
> $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
>
> I remember this is a version I downloaded from a link in FS archive.
>
> The ID for the one you sent to me is:
>
> $Id: mri_label2vol.c,v 1.34.2.4 2011/09/30 15:19:36 greve Exp $
>
> They look almost identical. Do you have any ideas what else may cause
> this issue and possible workaround?
>
> Thank you
>
> Leon
>
>
> *From:* Douglas Greve <greve@nmr.mgh.harvard.edu>
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Sent:* Friday, June 1, 2012 11:29 PM
> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
> transfer ic2.tri
>
>
> What version are you using? I fix a problem last Sept that might be
> like this. I've put a new version of mri_label2vol here:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol.linux
> Try this and let me know if it works.
> doug
>
>
> On 6/1/12 10:46 PM, Leon wrote:
>> Hi, Bruce
>> Here are my two command lines
>> For transferring the annot from the source template to the target
>> subject:
>>
>> /home/freesurfer/bin/mri_surf2surf --srcsubject ${srcsubject}
>> --sval-annot rh.ic2.annot --trgsubject ${trgsubject} --trgsurfval
>> src_2_trg.annot --hemi rh --surfreg sphere.reg0
>>
>> Where sphere.reg0 is the registration from the target subject to the
>> source subject.
>>
>> For transfer them to the volume file:
>>
>> /home/freesurfer/bin/mri_label2vol --annot src_2_trg.annot --temp
>> ${fs_dir}/${trgsubject}/mri/brain.mgz --subject ${trgsubject} --hemi
>> rh --fillthresh 0 --proj frac 0.3 0.8 0.05 --o src_2_trg_annot.mgz
>> --identity
>>
>>
>> Here is output for one of my transformations:
>>
>> Setting mapmethod to nnf
>> Source registration surface changed to sphere.reg0
>> Target registration surface changed to sphere.reg0
>> srcsubject = MacaqueA
>> srcval    = (null)
>> srctype    =
>> trgsubject = MacaqueB
>> trgval    =
>> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>> trgtype    =
>> srcsurfreg = sphere.reg0
>> trgsurfreg = sphere.reg0
>> srchemi    = rh
>> trghemi    = rh
>> frame      = 0
>> fwhm-in    = 0
>> fwhm-out  = 0
>> label-src  = (null)
>> label-trg  = (null)
>> OKToRevFaceOrder  = 1
>> Reading source surface reg
>> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.sphere.reg0
>> Loading source data
>> Reading surface file
>> /home/freesurfer/freesurfer/subjects/MacaqueA/surf/rh.orig
>> reading colortable from annotation file...
>> colortable with 162 entries read (originally
>> /usr/local/freesurfer/lib/bem/ic2.tri)
>> Reading target surface reg
>> /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.sphere.reg0
>> Done
>> Mapping Source Volume onto Source Subject Surface
>> surf2surf_nnfr: building source hash (res=16).
>> Surf2Surf: Forward Loop (61916)
>>
>> Surf2Surf: Dividing by number of hits (61916)
>> INFO: nSrcLost = 17467
>> nTrg121 = 61916, nTrgMulti =    0, MnTrgMultiHits = 0
>> nSrc121 = 35292, nSrcLost = 17467, nSrcMulti = 28910, MnSrcMultiHits
>> = 0.920927
>> Saving target data
>> Converting to target annot
>> Saving to target annot
>> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>> step2: writing the surface label to volume...
>> Number of labels: 0
>> Annot File:     
>> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>> Template Volume:
>> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/brain.mgz
>> Outut Volume:
>> /home/freesurfer/freesurfer/subjects/MacaqueB/mri/rh_MacaqueA_to_MacaqueB_fill0_porjs0.3_proje0.8_projin0.05.mgz
>> Registration File: (null)
>> Fill Threshold: 0
>> Label Vox Vol:  1
>> ProjType:      frac
>> ProjTypeId:    2
>> ProjStart:      0.3
>> ProjStop:      0.8
>> ProjDelta:      0.05
>> Subject:  MacaqueB
>> Hemi:    rh
>> UseNewASeg2Vol:  1
>> DoLabelStatVol  0
>> $Id: mri_label2vol.c,v 1.38 2011/09/30 15:17:59 greve Exp $
>> Template RAS-to-Vox: --------
>> -1.000  -0.000  -0.000  160.000;
>> -0.000  -0.000  -1.000  160.000;
>> -0.000  1.000  -0.000  160.000;
>> -0.000  -0.000  -0.000  1.000;
>> Template Voxel Volume: 1
>> nHits Thresh: 0
>> Using Identity Matrix
>> RegMat: --------
>>  1.000  0.000  0.000  0.000;
>>  0.000  1.000  0.000  0.000;
>>  0.000  0.000  1.000  0.000;
>>  0.000  0.000  0.000  1.000;
>> Label RAS-to-Vox: --------
>> -1.000  0.000  0.000  160.000;
>>  0.000  0.000  -1.000  160.000;
>>  0.000  1.000  0.000  160.000;
>>  0.000  0.000  0.000  1.000;
>>  INFO: loading surface 
>> /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.white
>> nvertices = 61916
>> Reading thickness
>> /home/freesurfer/freesurfer/subjects/MacaqueB/surf/rh.thickness
>> Loading annotations from
>> /home/freesurfer/freesurfer/subjects/MacaqueB/label/rh.MacaqueA_to_MacaqueB.annot
>> reading colortable from annotation file...
>> colortable with 162 entries read (originally
>> /usr/local/freesurfer/lib/bem/ic2.tri)
>> annotidmax = 162
>> Allocating Hit Volume (1013448704) voxels
>> nlabels = 162
>>
>> PVF (null)
>> Thesholding hit volume.
>> mri_label2vol done
>>
>> *From:* Bruce Fischl <fischl@nmr.mgh.harvard.edu>
>> <mailto:fischl@nmr.mgh.harvard.edu>
>> *To:* Leon <leonado78@yahoo.com> <mailto:leonado78@yahoo.com>
>> *Cc:* FreeSurfer <freesurfer@nmr.mgh.harvard.edu>
>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>> *Sent:* Friday, June 1, 2012 8:02 PM
>> *Subject:* Re: [Freesurfer] missing ROI when using mri_label2vol to
>> transfer ic2.tri
>>
>> Can you send us your command lines and screen output?
>>
>>
>>
>> On Jun 1, 2012, at 7:44 PM, Leon <leonado78@yahoo.com
>> <mailto:leonado78@yahoo.com>> wrote:
>>
>>> Hi, folks
>>>
>>> when I transferred the annotation file obtained using
>>> mri_make_face_parcellation based on ic2 (162 labels) to a volume
>>> file using mri_label2vol, I found that one ROI patch was missing in
>>> the volume file (see attached). I searched archives and the closest
>>> thread I could found is that somebody reported an ROI with the last
>>> index was missing in the mgz file after they were transferred from
>>> the annotation file to the volume file.
>>>
>>> Could someone help on this? If this happens to be a bug, is there
>>> any other strategy that will allow me to get a GM/WM ribbon without
>>> a hole on it?
>>>
>>> Many thanks in advance
>>> Leon
>>> <MissingROI.jpg>
>>> _______________________________________________
>>> Freesurfer mailing list
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>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
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>>
>>
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> HelpLine at
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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