Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

initial processing in devel 6.0 version and final stats processing in stable version 6.0?
by Lara Foland-Ross 28 Mar '16

28 Mar '16

Hi Freesurfer experts, We'd like to begin a cortical thickness and hippocampal subfield analysis in the most recent devel version of FS. Can you please confirm that we will we be able to run the analysis of these data in the final stable release of 6.0? Thanks, Lara Lara Foland-Ross, Ph.D. Research Associate Center for Interdisciplinary Brain Sciences Research Stanford University School of Medicine 401 Quarry Road, Room 1356 Stanford, CA 94305-5795

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(no subject)
by stdp82＠virgilio.it 28 Mar '16

28 Mar '16

Hi,I'm wondering whether the FS-FAST performed bandpass filtering. Stefano

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improving white/grey segmentation in recon -all for better volume estmation
by Ramtilak Gattu 28 Mar '16

28 Mar '16

Hello all, We have run recon -all on some healthy control subjects T1 images but we found out that the gray-white segmentation on half our subjects is bad and it leads to increased white matter volumes and decreased gray matter volumes. I have included a snap shot showing the difference in segmentation from bad to good for 3 cases https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts… . The parameter in the sequence are TE=4.92 ms, TR=19 ms, Flip angle =20 degrees. and use a snapshot one slice to show the good CNR. We are using Freesurfer version 5.3. Thanks Regards Tilak.

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FS-FAST bandpass filtering
by stdp82＠virgilio.it 26 Mar '16

26 Mar '16

Hi,I'm wondering whether the FS-FAST performed bandpass filtering. Stefano

1 0

getting started
by david sandeman 26 Mar '16

26 Mar '16

Hi I am a neurosurgeon working with robotics I have recently purchased a new macbook pro, running version 10.11.3 of OS X El capitan, speficially to run free surfer and other sofrtware designed to enhance my 3D segmentation capability The downloads I have tried only allow me to load freeview automatically. can you advise me how to set free surfer up on my mac or refer me to a download that will load the software automatically kindest david sandeman

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Is it possible to use the mris_make_face_parcellation with the ico6 mesh?
by Michael Waskom 25 Mar '16

25 Mar '16

Hi Freesurfers, I'd like to use mris_make_face_parcellation to downsample an individual subject's surface mesh to a resolution similar to fsaverage6. My understanding is that mris_make_face_parcellation should let me do this, and it does what I expect with ic3-5. However when I run it with ic6 as the target, it fails: [surf]$ mris_make_face_parcellation lh.sphere $FREESURFER_HOME/lib/bem/ic6.tri ../label/lh.ico6.annot Reading lh.sphere Reading /share/awagner/software/freesurfer/v5.3.0/lib/bem/ic6.tri parcellating hemisphere into 40962 units INFO: CTABunique() could not find a unique set in 10 tries INFO: CTABunique() could not find a unique set in 100 tries ERROR: could not find a unique color table I don't really care if the colors themselves are distinct, and it should be possible to just programmatically generate a valid color table (since 255 ^ 3 > 40962). I thought that providing a colortable with unique values through the -ctab option might work, but looking at the source code it seems that option will *write* a colortable, not read one. So, is there any way to accomplish the downsampling I want? Thanks in advance, Michael

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voxel size issue
by Hibert, Matthew Louis 25 Mar '16

25 Mar '16

Hi Freesurfer developers, Some structural images I'm working with only display properly in the axial plane, in which they were acquired; the sagittal and coronal views are distorted and appear stretched out in the superior-inferior direction, screenshots of this are attached. Freesurfer (both freeview and mri_info/mri_convert) incorrectly read the superior-inferior voxel dimension as 19mm when it is in fact 0.5mm. Reading the header with matlab shows that the header correctly specifies "slice thickness" as 0.5mm. There is another field, gap between slices, which has a value of 19mm, and freesurfer appears to be reading this field instead of the slice thickness field. This problem exists in both version 5.3 and the current dev version. The images display correctly in all 3 planes on both the MRI console computers and in Osirix. Is there a way to have Freesurfer read the slice thickness field instead so the images will display properly? I can point you to some data with this issue if that would be helpful. Thanks, Matt

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Gray-white segmentation
by Dr. Benson 25 Mar '16

25 Mar '16

I'm new to FreeSurfer. Trying to do volumetric analysis on MPRAGE data but on half of the studies the results are poor. Specifically, the gray matter volume is very small due to a poor segmentation of the white matter which includes much of the cortical gray matter. The contrast to noise is good and not sure why I got a good result on some and not others. Could use some help on this, please. Randy Benson, M.D. -- Medical Director--Center for Neurologic Studies *43000 W. 9 Mile Road * *Novi, MI 48375* *CNS Phone (248)277-3334* *Cell: (248) 227-9814* *Fax (586) 566-0178* Web: www.NeurologicStudies.com <http://www.neurologicstudies.com/> -- ***NOTICE*** The documents accompanying this email transmission contain confidential information belonging to the sender, which is legally privileged. The information is intended only for the use of the individual(s) or entity(ies) named above. If you are not the intended recipient, you are hereby notified that any disclosure, copying, distribution, or the taking of any action in reliance on the contents of this emailed information is strictly prohibited. If you have received this email in error, please immediately notify us by telephone at 248-277-3334 to arrange for return of the original documents to us. Thank you.

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FSFAST mkcontrast-sess with spmhrf 2 question
by Joseph Dien 25 Mar '16

25 Mar '16

Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com//

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Cortical thickness average
by Sahil Bajaj 25 Mar '16

25 Mar '16

Hello FreeSurfer community, I calculated cortical thickness for 100 controls following the instructions described here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness So I have 100 lh.thickness.fsaverage.mgh, one for each subject. I was wondering if there is any way to average the thickness over these 100 lh.thickness.fsaverage.mgh files to get one final lh.thickness.fsaverage.mgh I am interested in calculating cortical thickness for 15 previously defined ROIs, but I do not want to calculate 15x100 text files using mri_segstats i.e. 15 text files for each subject and then average over those but I would rather prefer to average over 100 lh.thickness.fsaverage.mgh files first and then calculate thickness for each ROI to get 11 text files. Any help would be really appreciated. Thanks, Sahil -- ------------------------------------------------- Sahil Bajaj Post-doctoral Fellow Nantz National Alzheimer's Center, Department of Neurology The Houston Methodist Research Institute (THMRI) Houston, TX, USA. E-mail:sahil.brain@gmail.com <E-mail%3Asahil.phy(a)gmail.com>

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