Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Problem of size
by Andrea Tateo 09 Apr '14

09 Apr '14

Hi FreeSurfer expert,I have a problem with command "recon-all". In recon-all.log I can read:«The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume.The resulting volume will have 312 slices.If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu).xn--i-nda hope are there anyone to help me.Thank for your help.Andrea

2 1

Intermediate stages of cortical inflation
by Xuelong Zhao 09 Apr '14

09 Apr '14

Hi, I would like to ask whether it is possible to display different levels of cortical inflation? I have been using the command: mris_inflate but the -dist and -n flags do not seem to make that much difference. Also, if I use fsaverage lh.orig as the input file and using the default options for mris_Inflate I don't seem to be able to recover the lh.inflated surface. Are there any alternative commands to control the level of inflation? Thanks.

2 1

Two positions (post-doc and software engineer) in Marseille, France
by Olivier Coulon 09 Apr '14

09 Apr '14

Dear all, we have two positions opening in Marseille, France. See documents attached. If interested, pease contact Dr Julien lefèvre at: julien.lefevre(a)univ-amu.fr Olivier Coulon -- Olivier Coulon, CNRS research Fellow, olivier.coulon(a)univ-amu.fr <mailto:olivier.coulon@univmed.fr> Tel: +33491828527 fax: +33491828550 http://olivier.coulon.perso.esil.univmed.fr <http://olivier.coulon.perso.esil.univmed.fr/> LSIS Laboratory, I&M Team ESIL, Campus de Luminy, Case 925, 13288 Marseille cedex 09, FRANCE BrainMorph logo http://www.lsis.org/brainmorph

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QDEC ANALYSIS
by Walton, Matt 08 Apr '14

08 Apr '14

Hello Freesurfer experts. I am trying to run a QDEC analysis on some MRI data I have. I want to see if thickness is correlated with language scores I have for each subject, while accounting for differences in age, and gender. I would like to select the gender as a fixed variable, and both the age and language scores as continuous variables, however the QDEC GUI will not allow me to select more than one continuous variable at a time (from what I've read on the website/mailing list I should be able to select up to two. Any idea of what might be wrong here, and how I can fix it. Thanks So much, Matthew Walton

2 1

Export freesurfer data
by ye tian 08 Apr '14

08 Apr '14

Dear Freesurfers, I would like to do some customized model fitting for cortical thickness. Is there a way to export freesurfer data into R or simply as a text? Thank you very much! Sincerely, Ye

3 7

restrain range when calculating subcortical volumes, such as hippocampus
by Yu(余)Qijing(奇静) 08 Apr '14

08 Apr '14

Hi, I am wondering how can I get the volume of hippocampus within a certain range? Given that the most anterior and posterior part of hippocampus may be more susceptible to errors because of other structures like amygdala and fornix, so I am wondering if the measurement would be more reliable if the most anterior and posterior parts of it are excluded. For example, calculate the volume of hippocampus without the most anterior and posterior 4 slices? I guess I could calculate manually, by summing the product of area of hippocampus on every specific slice and the distance between slices. But where can I get the information about the area on every slice? And what is the distance between the two slices (if for the coronal view)? Does it depend on the original DICOM files, or does Freesurfer do some re-slicing during the reconstruction? Thank you very much! Best, QJ

1 0

Rat cortex Parcellation
by Craig, Michael 08 Apr '14

08 Apr '14

Hello, I have a question regarding the parcellation of the rat cortex. I am interested in parcellating the cortex into distinct regions using an atlas and then finding grey matter volumes for each region. I realize that Freesurfer is primarily meant to be used on human subjects, but is it possible to replace the MNI atlas with a rat atlas (like the LONI rat atlas) during the parcellation step? Thanks for your time and help. best wishes, Mike

2 1

Extract seed from resting state networks mask (Yeo and Buckner maps)
by Celine Louapre 08 Apr '14

08 Apr '14

Hi Freesurfer team I am running a functional connectivity analysis on resting state data, and I would like to use as seed the precuneus/posterior cingulate region as seen on fsaverage/label/${hemi}.Yeo2011_17Networks_N1000.annot. However, this region is part of the label 17Networks_16 comprising other regions. Is it possible to isolate this specific portion of the label to create a seed region for the connectivity analysis ? I tried to do it on tksurfer, drawing a path around the region but then I could not figure out how to extract this part of the label. Thank you very much for your help Best Celine -- Celine Louapre, MD-PhD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

2 1

Longitudinal Analysis Questions
by pfotiad＠nmr.mgh.harvard.edu 08 Apr '14

08 Apr '14

Hi FS community, I am using FS 5.3 to do a longitudinal analysis on some data of mine. I have manually edited some of the reconstructed scans (i.e. addition of control points and white voxels) where the reconstruction was not as precise: 1) Is the base template created from the recon-all -base command in the wiki preserving those edits or do I need to reapply them in the base template? I know that this has been answered for previous versions of FS but I was wondering whether anything has changed in more recent versions. 2) Is it ok to run the longitudinal analysis described in the wiki when my subjects have an unequal number of timepoints (i.e. one person has 3 different timepoints, whereas another one has five) or should they all have the same number of timepoints? Thanks in advance! Best, Panos

2 4

failed templates from longitudinal base step
by L. Koenders 08 Apr '14

08 Apr '14

Dear FreeSurfer people, I have a question regarding the longitudinal pipeline, because something goes very wrong with my output. A short summary of my project: I have 3Tesla data from two timepoints, consisting of 50 people, so 100 scans in total. I have two groups, a control and an experimental group (cannabis users). In FS v5.3.0, I ran all scans through the Cross pipeline, and made brainmask.mgz pial edits where necessary. So far so good. Subsequently, I ran all the scans (all the edited scans) through the Base pipeline. This is when I ran into troubles, because only 2 templates (out of the whole group) turned out all right. The surfaces of all other scans are skipping gyri (for an example see attachment template_surfs). The scans that turned out allright were the very first and very last one of my subjects, which i find suspicous. I could of course try editing all the templates using control points, however I have this feeling that something else is going wrong with the registration of baseline and follow up scan. Do you know if this is a common error, and if I can do anything to fix it? I hope you can help me! Thanks & best regards, Laura Koenders ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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