Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

standard surface area estimation
by Christine Fennema Notestine 22 Aug '08

22 Aug '08

Is the default surface area estimation for a given ROI (in the stats text output) based on the area of the triangles within a given ROI on the white matter surface? Thanks, Chris

2 1

Re: free surfer error
by vin 22 Aug '08

22 Aug '08

hi, i am new to freesurfer. I tried reconstruction three times, autorecon1 works fine, but autorecon2 gives same error. *recon-all -autorecon1 -subjid your_subject_name % worked fine. :) **recon-all -autorecon2 -subjid your_subject_name* % this gives following error came in 11/ 12 hours. error in mid anterior detected - correcting... > writing aseg with callosum to > to /p/54/structural/t1/mri/aseg.auto.mgz... > corpus callosum matter segmentation took 1.5 minutes > > cp aseg.auto.mgz aseg.mgz > > #----------------------------- --------------- > #@# Intensity Normalization2 Fri Aug 22 12:56:57 MEST 2008 > /p/54/structural/t1/mri > > *mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz > > using segmentation for initial intensity normalization > reading from norm.mgz... > mri_normalize: aseg volume aseg.mgz must be conformed > using MR volume brainmask.mgz to mask input volume... > unconformed source detected - conforming...* > Linux xx.xxx.de <http://buddha.neuro.rad.med.uni-tuebingen.de>2.6.25.11-97.fc9.i686 #1 SMP Mon > Jul 21 01:31:09 EDT 2008 i686 i686 i386 GNU/Linux > > *recon-all exited with ERRORS at Fri Aug 22 12:57:18 MEST 2008 > * and that is how the directory looks like. [xx@xx mri]$ ls aseg.auto.mgz aseg.mgz brainmask.mgz norm.mgz nu_noneck.mgz orig.mgz T1.mgz talairach_with_skull.log aseg.auto_noCCseg.mgz brainmask.auto.mgz mri_nu_correct.mni.log nu.mgz orig rawavg.mgz talairach.log transforms any one has any idea, where i am making mistake Thank you very much / dhanyabad ji vinod

2 1

Banksst
by Vina Goghari 21 Aug '08

21 Aug '08

Hi guys, In the freesurfer aparc.annot label what is the "banksst" region in the temporal lobe? Thanks, Vina

2 1

group analysis- problem with assembling the data
by Elif SIKOGLU 21 Aug '08

21 Aug '08

Hello I am trying to run the isxconcat-sess command. I keep getting the following error. It looks like it can not create this --mask-lh.mgh file, actually even DA1_coll250250-col250250 directory does not exist. Any ideas? Thanks ----------------------------------- /home/melifs/freesurfer/sessions/coll250250_study mri_vol2surf --mov /home/melifs/freesurfer/sessions/coll250250/DA1_coll250250/bold/coll250250///mask.nii --reg /home/melifs/freesurfer/sessions/coll250250/DA1_coll250250/bold/register.dat --trgsubject fsaverage --hemilh --interp nearest --noreshape --projfrac 0.5 --projfrac-avg 0 1 .2 --o ./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh srcvol = /home/melifs/freesurfer/sessions/coll250250/DA1_coll250250/bold/coll250250///mask.nii srcreg = /home/melifs/freesurfer/sessions/coll250250/DA1_coll250250/bold/register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface /home/melifs/freesurfer/subjects/DA1/surf/lh.white Done reading source surface Reading thickness /home/melifs/freesurfer/subjects/DA1/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0 0 1 vol2surf_linear: nhits = 136215/136215 2 0.2 0 1 vol2surf_linear: nhits = 136215/136215 3 0.4 0 1 vol2surf_linear: nhits = 136215/136215 4 0.6 0 1 vol2surf_linear: nhits = 136215/136215 5 0.8 0 1 vol2surf_linear: nhits = 136215/136215 Done mapping volume to surface Number of source voxels hit = 8269 Reading source surface registration /home/melifs/freesurfer/subjects/DA1/surf/lh.sphere.reg Done loading source registration surface Reading target registration /home/melifs/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (DA1 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (136215) Reverse Loop had 26091 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces mghWrite(./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh, -1): could not open file nSrc121 = 94106, nSrcLost = 0, nSrcMulti = 42109, MnSrcMultiHits = 2.27569 nTrg121 = 146432, nTrgMulti = 17410, MnTrgMultiHits = 2.49862 Writing to ./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh Dim: 163842 1 1 ------------------------------------ .... /home/melifs/freesurfer/sessions/coll250250_study mri_concat ./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/BC4_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/MB2_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/AJ_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/BG_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/MBA_coll250250-coll250250/--mask-lh.mgh ./coll250250/tmp-isxconcat0.5391-sess/GC_coll250250-coll250250/--mask-lh.mgh --o ./coll250250//lh.masks.nii mghRead(./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh, -1): could not open file ninputs = 7 Checking inputs ERROR: reading ./coll250250/tmp-isxconcat0.5391-sess/DA1_coll250250-coll250250/--mask-lh.mgh

2 1

Qdec Error
by nels5614＠umn.edu 20 Aug '08

20 Aug '08

Hello, I am seeing the following error in the terminal window when I run an analysis in QDEC: INFO: ignoring tag Creator INFO: ignoring tag SUBJECTS_DIR INFO: ignoring tag SynthSeed INFO: demeaning continous variables Continuous Variable Means (all subjects) Class Means of each Continuous Variable 1 groupfivecontrol 2 groupfivepatient WARNING: Marker for class groupfivecontrol was invalid. WARNING: Color for class groupfivecontrol was invalid. WARNING: Marker for class groupfivepatient was invalid. WARNING: Color for class groupfivepatient was invalid. ============================================================ Completed loading of analyzed data. ERROR: gdfOffsetSlope: variable number 0 exceeds max 0 I am looking for differences in cortical thickness between groups. Could this error be affecting my results? Regards, Miranda

1 0

brain orientation
by Margaret Sheridan 20 Aug '08

20 Aug '08

We are new users of freesurfer (linux v 4.0.5) and have the following question: We have some .4dfp.img MPRAGE files which we are trying to use (from Wash U). When we run recon_all (1st step) or mri_convert on its own, the brain comes up upside down as if it was rotated 180 degrees around the sagital plane (see attached picture of the 4dfp.img file viewed in scuba). Since when we view the original 4dfp.img file or the orig.mgz file they are both in this orientation it appears that this is a problem with the original files. If we use tkmedit to rotate the brain around the sagital plane once we're in .mgz format the recon steps (including normalization which, obviously, would fail previously when the brain was upside down) would complete fine. However I'd prefer to rotate these brains using mri_convert (or another program) so I can rotate the original files; which is why I'm writing now. To determine what the current orientation for these images was I opened the original files in scuba & ran MRI convert like this: mri_convert --in_orientation ASL -i vcXXX.4dfp.img --out_orientation ASL -o vcXXX.4dfp.ASL.img until I found an orientation which matched the original. The orientation which matched the original was ASL. In this step I just converted from one form to the same form to reduce confusion. Next I ran several versions of the following: mri_convert --in_orientation ASL -i vcXXX.4dfp.img --out_orientation SAR -o vcXXX.4dfp.SAR.img however no mater how I changed the 'out orientation' when the files were viewed in scuba they all appeared to have the same orientation as the original (ASL or rotated around the sagital plane). Is there any more documentation on re-orienting in mri_convert or does anyone have any ideas/experience that can help? Thanks, Margaret Sheridan Kathy Zhang

4 4

WM segmentation
by c.k.tamnes＠psykologi.uio.no 20 Aug '08

20 Aug '08

Hi Freesurfers, I have a couple of questions regarding WM segmentation. My dataset is a large healthy sample of children and adolescents (8-19 years old). Freesurfer 4.01 for linux has been used for processing. Firstly, in about 20% of my subjects there are some voxels segmented as WM isthmuscingulate located between thalamus and pallidum, seemingly not connected to the rest of WM isthmuscingulate located more posteriorly. See pictures for illustrations (marked with the cursor). Secondly, in many of my subjects (about 50%) a few voxels (usually fewer than 10) above hippocampus, next to ventralDC are segmented as parahippocampal WM. See cursor in last picture for an illustration. Does anyone have any experice with these problems or any suggestions on how do deal with them? Both problems could probably be solved with manual segmentation, but it would be very time consuming. Best regards, Christian -- Christian K. Tamnes Center for the Study of Human Cognition Department of Psychology, University of Oslo PB 1094 Blindern, 0317 Oslo, Norway Cell ph: (+47) 97572410

5 6

true-Talairach vs mni-Talairach?
by Steinmann, Iris 20 Aug '08

20 Aug '08

Dear Freesurfers, I am a little bit confused about the talairach coordinates in Freesurfer. I have two diffrent versions of Freesurfer: 4.0.1 and 4.0.5. I opend brain.mgz in tkmedit and try to do the following things: when I type in Freesurfer 4.0.1 in the tkmedit-window some Talairach coordinates, the numbers I typed change a bit. I think it is because tkmedit think that I gave mni-Talairach an modified them to true-talairach. Is this right? When I type the same in Freesurfer 4.0.5 the talairach-numbers I type in the window stay the same. So, can I be sure that Freesurfer 4.0.5 knows that I type the true-talairach(?), and show me the correct true-talairach-point in brain.mgz ? Thanks for your answers!

2 1

about cortical thickness
by 李日 20 Aug '08

20 Aug '08

Hi: I have run the recon-all command and it finished without error. And now I am interested with the thickness, I want to select a region of interest and get information of every voxel,including the coordinate ,the thickness of this voxel.Also , I want to put these information into a file. Does anyone know how to do this? Thank you very much. Tim

4 4

about the label file
by 李日 20 Aug '08

20 Aug '08

Hello: I select a region and save it to a label file named red.label. But I could't understand the data in this file. The follwing is part of this file. #!ascii label , from subject cengqinping vox2ras=TkReg coords=white 5690 31281 -51.356 -54.196 26.649 0.000000 31282 -52.142 -54.229 26.699 0.000000 31283 -52.709 -54.040 26.704 0.000000 31284 -52.913 -53.821 26.712 0.000000 31313 -50.128 -54.270 25.875 0.000000 31314 -50.598 -54.363 26.022 0.000000 31315 -51.471 -54.354 26.035 0.000000 31316 -52.222 -54.125 26.099 0.000000 (1).Does the number 31281 int the first row means the number of vertex? (2).what does (-51.356 -54.196 26.649) mean? (3),what does the zero at the end of row mean? (4).I want to get the thickness of every vertex, How can I do that? thanks in advance Tim

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