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PETSURFER Tutorial Problems <Repost>
by Anderson Napolitano 18 Jan '17

18 Jan '17

Good Afternoon Support Team, Per step one of your PETSURFER tutorial, the command: gtmseg --s <subject>?, where the <subject> is the name of the subject that we had ran recon-all, outputs the error as described in out.txt attached in this email. If you have the time, it would be much appreciated if you can help us resolve this issue. Thank you for your time. Warmest Regards, Anderson Napolitano?

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QDEC versus Terminal annotation
by Martin Juneja 18 Jan '17

18 Jan '17

Hi, I am comparing cortical thickness measures between controls and patients. I displayed the results in qdec. I found that cluster is showing significant difference in thickness between controls and patients (controls having more thickness than patients). In terminal, its showing output as: ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation 1 2.6021 130 1285.86 11.5 -89.5 21.1 1764 superiorparietal I am not an expert in anatomy but when looking at the cluster in qdec (please find it attached), it seems like the cluster is not superior parietal as shown in terminal and even TAL coordinates are not matching with standard superior parietal lobe coordinates. When I click on find cluster in qdec, shouldn't cursor on that cluster show the same area shown in terminal? Could you please share your thoughts on this, why the area displayed in terminal window is not matching with the one shown in qdec ? Thanks.

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Neuroimaging postdoctoral position
by Tiril Pedersen Gurholt 18 Jan '17

18 Jan '17

Dear All, At the NORMENT – K.G. Jebsen Research Centre for Psychosis Research, a Centre of Excellence, Institute of Clinical Medicine, University of Oslo, there is a position available as a postdoctoral student funded by the Research Council of Norway. The research area is psychiatric neuroimaging with focus on analysis of structural and functional, DTI and ASL MR imaging datasets with regard to developmental trajectories and genetic, environmental and phenotypic variation. Applicants should have a doctoral degree (PhD) in neuroimaging, computer science, bioinformatics, psychiatry, psychology or equivalent. Applicants who have handed in their dissertation for evaluation are also encouraged to apply, caveat the dissertation is approved. The application deadline is January 25, 2017. For further information and to submit an application please also see http://uio.easycruit.com/vacancy/1719677/70331?iso=no . Best regards, Tiril Gurholt --- Tiril Gurholt Postdoctoral Fellow Psychosis Research Centre, NORMENT Institute of Clinical Medicine, University of Oslo, Norway http://www.med.uio.no/norment/ [cid:image001.png@01D21DA0.544E82D0]

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recon-all error (Freesurfer)
by Gwang-Won Kim 18 Jan '17

18 Jan '17

1 0

FS Anatomic ROIs Atlas
by Da, Xiao 17 Jan '17

17 Jan '17

Dear Freesurfer Community, I am wondering if you have these anatomic ROIs (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation) already done for the 3D volumetric standard MNI brain (either ch2 single subject brain(preferred) or 152 average brain) Greatly appreciated it. Thanks and best regards, Xiao Da Biomedical Engineer - Programmer Analyst II Functional Neuroimaging Laboratory Brigham and Women's Hospital 221 Longwood Avenue, Braunwald Building, Room LM116 Boston, MA 02115 xda(a)bwh.harvard.edu<mailto:xda@bwh.harvard.edu>

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Anatomical ROI parcellation
by Aya Kabbara 17 Jan '17

17 Jan '17

Dear Freesurfer team, I am wondering is there a way using tksurfer to edit a given atlas (for example: destrieux atlas). I would like to parcellate the superior temporal region into three regions . Is there a way to do that? Thank you Aya

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Re: [Freesurfer] V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream
by Antonin Skoch 17 Jan '17

17 Jan '17

Dear Martin, thank you for the feedback. I read the wiki but the instructions concerning aseg edits were not much clear for me. And, I was misinformed by -noasegfusion option. The pity with aseg errors is that with the current design and when the error is large to affect surfaces in base, it is necessary to edit the same error twice. Since the aseg of base is not initialized from cross, and long is not initialized from base, then one has to edit the same error both in base and in long (or cross). If there is a systematic error which affects all timepoints (as it is in my case - I have 2 points), I effectively have to edit the same error 3 times. It is quite large error affecting whole posterior part of lateral ventricle (see screenshot). Therefore, I thought that best option would be to edit the base and initialize long from base using -noasegfusion. I tried to do that by manually copying aseg from base and manually running mri_ca_label with -r and -ri option (and and the error is (almost) cleaned in long. Why do you think that the initialization from base is worse/undesirable than initialization from fused aseg from cross? It seems to me that to initialize from fused (averaged) asegs of cross or initialize from aseg of base (which is averaged template of cross) is methodologically quite similar, should produce similar results and in terms of edits it is much more convenient way. Regards, Antonin Hi Antonin, the -noasegfusion is not really supported and a left over from initial testing when we first developed the stream. I will take a look at it and probably remove the flag (or implement it in a way that it really initializes with the aseg from the base, although I think this is not desirable, unless one really assumes there is no/ or very little change between time points. About aseg edits in longitudinal processing, please look at our edit wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz> “ ASEG edits can be done in cross, base and long. Recommendation: Edit in long only if you want to correct the volume of important structures. Edit in base if surfaces need to be changed due to incorrect labeling of aseg. Not necessary to edit in cross. The segmentation in the long runs is initialized with a fused aseg (a weighted average of the cross sectional asegs). Thus any edits done to the cross sectionals are incorporated indirectly into the long stream. But since the fused aseg is used only for the initialization, it can happen that manual edits from the cross get removed again. Therefore, to correct the volume, just edit the long." So for your ventricle correction, you could either clean up the cross data and hope it caries over to the long (it should), or directly edit the long aseg. Best, Martin > On 16 Jan 2017, at 23:23, Antonin Skoch <a...(a)ikem.cz> wrote: > > Dear experts, > > I am testing the longitudinal stream with V6beta version. > > The recon-all -help says for -noasegfusion: > > Do not create 'fused' aseg from the longbase timepoints, which would normally > be used to initialize the ca_labeling. Instead, initialize using the longbase > aseg.mgz. > > As I looked to recon-all code it seems that in case of -noasegfusion there is > no use of -r and -ri parameters and therefore no "initialization". Could you > please comment on? > > My second query is regarding manual edits: > > In one subject the manual editing of aseg was necessary due to ventricle > mislabeling. I edited the aseg.presurf in base template and subsequently run > longitudinal stream via > > recon-all -long tpID templateID -noasegfusion -all > > From the last sentence of -noasegfusion help I (wrongly) expected that my > aseg.presurf edits in base template would be incorporated for -long recon. > However, this was not the case, the edits have not been incorporated at all. > Looking at the recon-all code the aseg.presurf from base is never used for > -long. > > I thought that I could incorporate manual edits from base by manual copying > of aseg.presurf from base to long directory. As I looked for the way how the > manual aseg edits are handled in recon-all, they are identified by using the > difference between the files aseg.auto and aseg.manedit which contains manual > edits. Therefore I think that the copying from base is not an option, I > expect that this would replace segmentations not only in manual edit regions, > but in all regions where the aseg.auto of base and aseg.auto of -long differs > (they do not have the same input) which is undesirable. So I think I do not > have any other option than to edit aseg.presurf in -long again. > > Could you please comment on how to optimally handle such situations? > > Regards, > > Antonin Skoch > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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TRACULA in FreeSurfer 6.0 trac-paths error
by Derek A Pisner 17 Jan '17

17 Jan '17

Hi Anastasia, I am getting the following error when running trac-all –paths on all of my diffusion images using the newly updated TRACULA: *vlogin03.ls5(97)$* /work/04171/dpisner/stampede/Applications/freesurfer/bin/trac-all -no-isrunning -path -c /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/trac_config.txt niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm WARNING: niiRead(): unknown time units 0 in /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/dmri/dwi.nii.gz Any idea what’s going on here? Thanks as always, Derek Pisner Doctoral Student CLA 4.600 Mood Disorders Laboratory (MDL) Department of Psychology | The University of Texas at Austin P.S. Here is the header information on my dwi.nii.gz file: *vlogin03.ls5(105)$* fslhd dwi.nii.gz filename dwi.nii.gz sizeof_hdr 348 data_type FLOAT32 dim0 4 dim1 115 dim2 115 dim3 56 dim4 55 dim5 1 dim6 1 dim7 1 vox_units Unknown time_units Unknown datatype 16 nbyper 4 bitpix 32 pixdim0 0.000000 pixdim1 2.000000 pixdim2 2.000000 pixdim3 2.000000 pixdim4 1.000000 pixdim5 1.000000 pixdim6 1.000000 pixdim7 1.000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Unknown qform_code 0 qto_xyz:1 2.000000 0.000000 0.000000 0.000000 qto_xyz:2 0.000000 2.000000 0.000000 0.000000 qto_xyz:3 0.000000 0.000000 2.000000 0.000000 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Aligned Anat sform_code 2 sto_xyz:1 -2.000000 0.000000 0.000000 114.551003 sto_xyz:2 0.000000 2.000000 0.000000 -74.456001 sto_xyz:3 0.000000 0.000000 2.000000 -0.960182 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior file_type NIFTI-1+ file_code 1 descrip aux_file -- Derek Pisner

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V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream
by Antonin Skoch 17 Jan '17

17 Jan '17

Dear experts, I am testing the longitudinal stream with V6beta version. The recon-all -help says for -noasegfusion: Do not create 'fused' aseg from the longbase timepoints, which would normally be used to initialize the ca_labeling. Instead, initialize using the longbase aseg.mgz. As I looked to recon-all code it seems that in case of -noasegfusion there is no use of -r and -ri parameters and therefore no "initialization". Could you please comment on? My second query is regarding manual edits: In one subject the manual editing of aseg was necessary due to ventricle mislabeling. I edited the aseg.presurf in base template and subsequently run longitudinal stream via recon-all -long tpID templateID -noasegfusion -all >From the last sentence of -noasegfusion help I (wrongly) expected that my aseg.presurf edits in base template would be incorporated for -long recon. However, this was not the case, the edits have not been incorporated at all. Looking at the recon-all code the aseg.presurf from base is never used for -long. I thought that I could incorporate manual edits from base by manual copying of aseg.presurf from base to long directory. As I looked for the way how the manual aseg edits are handled in recon-all, they are identified by using the difference between the files aseg.auto and aseg.manedit which contains manual edits. Therefore I think that the copying from base is not an option, I expect that this would replace segmentations not only in manual edit regions, but in all regions where the aseg.auto of base and aseg.auto of -long differs (they do not have the same input) which is undesirable. So I think I do not have any other option than to edit aseg.presurf in -long again. Could you please comment on how to optimally handle such situations? Regards, Antonin Skoch

2 1

T2 voxel size needed for recon_all
by Erik O'Hanlon 17 Jan '17

17 Jan '17

2 2

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