Freesurfer

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30083 discussions

Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking
by N. Eiji Nawa 26 Aug '08

26 Aug '08

Thanks for the clarification, Sebastian! (I am sending this to the ML hoping that your reply might be useful to other newbies like me!) E. On 2008/08/26, at 16:41, Sebastian Moeller wrote: > Hi Eiji, > > > On Aug 26, 2008, at 3:22 AM, freesurfer-request(a)nmr.mgh.harvard.edu > wrote: > >> Message: 2 >> Date: Tue, 26 Aug 2008 10:21:30 +0900 >> From: "N. Eiji Nawa" <eiji(a)atr.jp> >> Subject: Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain >> masking >> To: freesurfer(a)nmr.mgh.harvard.edu >> Cc: Doug Greve <greve(a)nmr.mgh.harvard.edu> >> Message-ID: <8400CC61-80F1-488D-8CE8-BB0C4463A598(a)atr.jp> >> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed >> >> A follow-up to my own post. I found a post that suggested that >> executing 'spatialsmooth-sess' with the '-update' could prevent the >> generation of fmcsm5.nii (https://mail.nmr.mgh.harvard.edu/ >> pipermail// >> freesurfer/2008-July/008081.html). > Nah, the July result was that OSX's "test" command does not behve > like the gnu "test" used in Linux, and therefore -update will not > work properly on macs. So running without the -update flag is one > possible work around. > > Well, actually running "preprocess-sess" with the "-noupdate" > command line option should solve your problems for now... > > >> >> >> In fact, running: >> >> spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s mgh-101.1 -d >> $FSFTUTDIR/my-study -noinorm >> >> worked fine! > As expected... > >> >> >> Likewise with 'mkbrainmask-sess': >> >> mkbrainmask-sess -maskstem brain -fsd bold -s mgh-101.1 -d >> $FSFTUTDIR/ >> my-study >> >> _without_ the '-update' correctly generated the masks/brain.nii >> volume. >> >> I just wonder if preproc-sess only has this behavior in systems like >> mine, since it does not look like it is a general problem (I am using >> Mac OS 10.4.11 in a PowerPC G5). > It seems Macos 10.4.11 as well as Macos 10.5.4 are affected. I > would not be amazed, if all versions of MacosX are affected, as of > their BSD origin compared to Linux's gnu core utilities. > The details: While "test $infile -nt $outfile" returns 0 under > Linux, if $outfile does not exist, it returns 1 under Macosx. This > is hard to generically care for... > > >> >> >> In any case, running spatialsmooth-sess and mkbrainmask-sess manually >> after executing preproc-sess seems to generate all the volumes! > A (potentially incomplete) list of affected fs-fast scripts: > /fsfast/bin/mc-sess > ./fsfast/bin/mkbrainmask-sess > ./fsfast/bin/mktemplate-sess > ./fsfast/bin/preproc-sess > ./fsfast/bin/spatialsmooth-sess > ./fsfast/bin/stc-sess > > Ahoi > Sebastian > >> >> >> E. > > -- > Sebastian Moeller > > Tel.: 04 21 - 2 18 - 90 96 > Fax.: 04 21 - 2 18 - 90 04 > GSM: 0 15 77 - 1 90 31 41 > moeller(a)neuro.uni-bremen.de > > AG Kreiter / FB 2 > Institut fuer Hirnforschung III > Abteilung Theoretische Neurobiologie > Universitaet Bremen > Biogarten > Hochschulring 16a > Postfach 33 04 40 > 28359 Bremen > > > > >

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recon with only 1 mprage?
by jake＠nmr.mgh.harvard.edu 25 Aug '08

25 Aug '08

Hi! Can anyone tell me what possible issues there are with only using one mprage in creating a recon? [Our first mprage is crashing the reconstruction, and we have found that there was an error of some sort during that mprage, thus the need to do the recon with only the second mprage.] Thanks in advance, Jake

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custom templates and mris_make_template options
by Jan Kalkus 24 Aug '08

24 Aug '08

Hi everyone, We're making a template to register some monkey brain surfaces to. I've written a script based on instructions from the Surface Registration and Templates page ( http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates ) on FreeSurfer wiki. I'm stuck at "Round 1" with the "mris_make_template" command. In the first step we used: mris_make_template \ lh sphere \ bu_edited bs_edited vi_edited \ lh.monk_temp_all.tif As there were no *h.sphere.reg files yes, we used the *h.phere surfaces. My question is, for the next "mris_make_template" should we use the same (*h.sphere) surface or use the newly created *h.sphere.reg surfaces to create the template? mris_make_template \ lh sphere.reg \ bu_edited bs_edited vi_edited \ lh.monk_temp_all.tif Has anyone else used this process to create their own templates/ registered surfaces? Does anyone have any suggestions? Thanks. - Jan Kalkus

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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

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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

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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

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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

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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

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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

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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

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