Freesurfer

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30132 discussions

IndexError: list index out of range in post-processing of longitudinal data
by Sandra Preissler 25 Jun '13

25 Jun '13

Dear freesurfer users, we wanted to do longitudinal analyses for two different time points. So we did the longitudinal processing as described in the tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#Prepa…) The "Post-Processing Longitudinal Data" step does not work. (long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage ) After starting the process we get the following error message: Parsing the qdec table: ./qdec/long.qdec.table.dat Traceback (most recent call last): File "/opt/freesurfer/bin/long_mris_slopes", line 521, in <module> qdectable = LongQdecTable(options.qdec) File "/srv/freesurfer/bin/LongQdecTable.py", line 30, in __init__ self.parse(stpmap) File "/srv/freesurfer/bin/LongQdecTable.py", line 58, in parse if strlst[0].upper() == 'SUBJECTS_DIR': IndexError: list index out of range Weve already tried a lot of things, like removing subjects from the longitudinal qdec table, except for one subject, or deleting every command that was optional, but it still does not work. The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64 Can you help us in fixing this problem? Thanks in advance! Sandra ---------------------------------------------------------------- This message was sent through https://webmail.uni-jena.de

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freesurfer registration
by Parker, Christopher 25 Jun '13

25 Jun '13

Hi, I understand that the recon-all script registers and then averages two anatomical images (after bias field correction) if two are provided in the "orig" folder, before performing the other parcellation stages. I am writing a report and it might be good to mentioned what registration is used. I'm guessing this is a rigid registration using sum of squared differences cost function? Best, Chris

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Matrix building
by Linn Mittlestein 25 Jun '13

25 Jun '13

Hello, I wondering if possible using fsgd files to do group analysis with two factors (one with 3 levels, one with 2 levels), with one covariate. On fsgd example list I cannot find this example? Kind Regards, Linn

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Re: [Freesurfer] ribbon label volume mapping
by Colin Reveley 25 Jun '13

25 Jun '13

Doug - thanks that sounds well worth trying. the labels we have have arbitrary spatial resolution in the saggital plane, and 1mm gaps between saggital slices. In general in this project we are using an isotropic resolution of 0.25mm. To generate surfaces in freesurfer I have to downsample to 0.35mm (to fit into 256) in applying the procedure you suggest a) is it possible to use a volume with a dimension > 256? b) is it possible to use a non-isotropic resolution? playing around with non-isotropic resolutions, projection fractions and vote would yield different results. c) can mri_aparc2aseg output a volume > 256? 0.35 isotropic will be ok. we'd prefer 0.25 if we can. best Colin > ---------- Forwarded message ---------- > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > To: <freesurfer(a)nmr.mgh.harvard.edu> > Cc: > Date: Sun, 23 Jun 2013 20:03:09 -0700 > Subject: Re: [Freesurfer] ribbon label volume mapping > > You could run mri_vol2surf at different projection fractions (and using > nearest neighbor interp). This will create a set of files, one for each > projection fraction. You can then run mri_concat with the --vote option to > get you the most frequently occurring label. You could then use > mris_seg2annot to create an annotation. > > If you want to go the other way, you will need to combine your labels into > an annotation (mris_label2annot), then convert that into a volume with > mri_aparc2aseg. > > doug > > > On 6/22/13 10:08 AM, Colin Reveley wrote: > > If one has a volume of integers, each representing a cortical area, > can one map that to the surface as a set of labels, in a smart way that > e.g. takes the mode of the voxels that lie on the vector between equivalent > white and pial nodes (ie uses curvature and thickness information, tacitly > or explicitly)? > > the labels are not exactly on the ribbon. There are many voxels outside > the ribbon that are non zero. Like caudate etc. > > and some voxels that are within the ribbon but are zero because the > label data is was/is non-isotropic originally (which is the problem we want > to solve in fact). > > that would be great. > > Now let's say you already have labels on a mesh. > > can you generate a ribbon volume of labels, i.e. the opposite operation > to what I enquire about above (opposite but not inverse operation)? > > This is work in rhesus. So my pipeline is very barebones indeed, really > just > > mri_normalize > ... > mri_tesselate > mri_inflate/smooth/sphere > mris_fix_topology <-noaseg -noaprc> > mris_make_surfaces <-naseg -noaparc> > > I only have access to what is generated by that sequence or what I can > subsequently generate. > I can generate a freesurfer like ribbon with mris_fill. > > My understanding of labels and data mapping in general in freesurfer is > very poor. > > Maybe adapting one of your matlab scripts might be an idea, if there is > not another way? > > many thanks, > > Colin, > Sussex > > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >

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Monte Carlo simulation: Talairach coordinates
by Emily Boeke 25 Jun '13

25 Jun '13

Hi All, I'm running Monte Carlo simulations on functional data, and the coordinate information outputted in the cluster.summary file isn't making sense. Usually the coordinates for the clusters listed are Talairach coordinates, but in the .summary files I'm getting, the coordinates are labeled "VoxX VoxY VoxZ" instead of "TalX TalY TalZ" and the numbers are clearly not Talairach coordinates. Above the table, it says "Reporting Coordinates in Voxel Indices." I also noted that in the descriptive information above the table, it says "Registration: None: Tal Coords invalid." However, the .nii files I'm seeing look like I would expect them too. I'm using the same command line I've run before, so I have no idea why the .summary file looks different. Does anyone know why this would be? Thanks, Emily

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problem with surface area regression
by wen.zhang55 25 Jun '13

25 Jun '13

Dear Freesurfer, I have checked the mail list, none could answer my problem. I added up the value of all vertxes in the .area or .area.pial files, find that brain size did not contribute much to that vertex-sum. However, some experiment used total brain volume as a regreesion coefficient to remove brain size effect. In these case, with the comparison of surface area in vertex-to-vertex, is it proper to use the above vertex-sum as the regression coefficient to remove different brain size? Thank you very much! Cowen 2013-06-24 wen.zhang55

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freeview: create ROI in inflated surface
by Garikoitz Lerma-Usabiaga 25 Jun '13

25 Jun '13

Hi list, is it possible to create a ROI in an inflated surface within freeview or do I have to use tksurfer? It seems that I only can edit volume files. After exploratory mri_glmfit, I want to outline a ROI in fsaverage inflated surface and afterwards create a label to obtain CT averages per every subject. Many thanks! Gari

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fsaverage vertex index to talairach
by Cesar Echavarria 25 Jun '13

25 Jun '13

Hello, Anyone know of a fast way to get the talairach coordinates of a vertex index in fsaverage. A function or script is best since I want to do this for a large number of vertices. Thank you for any help you guys can provide. Cesar

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Fwd: DTI questions
by Rotem Saar 24 Jun '13

24 Jun '13

Hi there, Long time:). Well I wrote to the list several times regarding high FA values I got when performing DTI analysis. Today we know that the problem was an additional direction (we had 17 directions instead of 16 - we used a Philips scanner,1.5T). So we deleted the additional slices and the high values indeed disappeared, but then another problem came up (tried several subjects so the problem is not specific to a subject) - I noticed an artifact that I can't explain - please see the attached pictures. This artifact existed even before I deleted the additional slices, also - I see the artifact also when loading the masked volume...It is cyclic - run over all slices... any ideas ? I'm using version 5.2 and I know the command lines are correct (send it to u in the past). Thanks for your help Rotem

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Multiple inputs into recon-all -i
by ye tian 24 Jun '13

24 Jun '13

Dear David, I wonder whether there is a short cut for recon-all -s Barbara -i /path_to_data/scan1.dicom -i /path_to_data/scan2.dicom ... -i /path_to_data/scan100.dicom Recon-all -i takes only a single file as an input. A typical user, however, has hundreds of files for a particular subject. For example, the directory Barbara may have 100 scans. Therefore, the above command is necessary to include all the scans. I understand that I can write loops to a text file and then copy and paste to command line. However, I wonder whether there is a simpler way to input several files or even a directory to recon-all. Thank you very much! Sincerely, Ye

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