Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

HippocampalSubfields only generates lh
by Jiook Cha 22 Jan '16

22 Jan '16

Hi Iglesias, I recently tried HippocampalSubfields in freesurfer 6.0. It only completed hippocampal segmentation for the left hemisphere, but not the right. Under scripts folder, recon-all.error says: /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/recon-all PWD /ifs/scratch/pimri/posnerlab/1anal/osa/fs2/B03/label CMD /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/bin/segmentSF_T1.sh /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer/MCRv80 /ifs/scratch/pimri/posnerlab/freesurfer_dev/freesurfer B03 /ifs/scratch/pimri/posnerlab/1anal/osa/fs2 left So it seems as left hippocampus failed the pipeline didn’t try the right hippocampus. Attached is hippocampal-subfields-T1.log. Do you have any idea what’s happening here? Best, Jiook

2 4

Centroid of a binary volume question
by pfotiad＠nmr.mgh.harvard.edu 22 Jan '16

22 Jan '16

Dear FS Community, I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help! Best, Panos

1 0

LME results - Talairach coordinate, surface area
by Hanbyul Cho 22 Jan '16

22 Jan '16

Dear FreeSurfer Team, I am wondering how I can report Talairach coordinate and cluster size (=surface area, mm^2) of the LME corrected results. We can count the each clusters' number of vertices on fsaverage template by checking the *.label. (is it right?) However, I don't know how we can the clusters' talairach coordinate and the cluster size of LME results. This results form differed from GLM results form of Freesurfer. Could you let me know the method of calculation the clusters coordinate and size after LME analysis by LME MATLAB tool? Best Regards, Han.

1 0

(no subject)
by Erik Lindberg 22 Jan '16

22 Jan '16

I just want to investigate significant correlation with the csf variable correcting for apoe-status, gender, diagnosis and age below previous correspondence your classes are right. What are you trying to test with your contrast matrix? On 01/20/2016 05:33 AM, Erik Lindberg wrote: > Dear Freesurfers, > > I am running a design in which I want to correct for a number of > categorical variables: diagnosis, gender and apoe status and one > continuous variable (age) in a correlation analysis > > Did I get this right? (below) > > Thanks, Eric > > GroupDescriptorFile 1 > > Title MyTitle > > Class AMCI_F_APOE- > > Class AMCI_F_APOE+ > > Class AMCI_MALE_APOE- > > Class AMCI_MALE_APOE+ > > Class CTL_FEMALE_APOE- > > Class CTL_FEMALE_APOE+ > > Class CTL_MALE_APOE- > > Class CTL_MALE_APOE+ > > Class NON_A_MCI_FEMALE_APOE- > > Class NON_A_MCI_FEMALE_APOE+ > > Class NON_A_MCI_MALE_APOE- > > Class NON_A_MCI_MALE_APOE+ > > Class SCI_FEMALE_APOE- > > Class SCI_FEMALE_APOE+ > > Class SCI_MALE_APOE- > > Class SCI_MALE_APOE+ > > Variables AGE_DEMEAN CSF_Ab40_ADx > > > With the contrast matrix: corr.mtx: > > 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 > 1 1 1 1 1 1 1 1 1 1 1 1 1 > > > > _______________

1 0

(no subject)
by Erik Lindberg 22 Jan '16

22 Jan '16

I just want to run plane correlation with the csf-variable best Eric

2 1

asegstats2table for all subjects in the directory
by Luis Fernado Silva Castro de Araújo 22 Jan '16

22 Jan '16

Hi Freesurfer experts, I wonder if there is a way of extracting the stats for all patients in my last run at the same time. I have around 120 observations and the asegstats2table syntax works in such a way that all the patients names should be listed: asegstats2table --subjects 004 021 040 067 080 092 \ --segno 11 17 18 \ --tablefile aseg.vol.table I hope I am wrong, but it seems that the —subjects argument does not accept substitution with wildcards, like * or *.* Is there a way to make the command run the extraction of the statistics in all subjects within the $SUBJECTS_DIR in order to avoid typing all the 120 folder names? A bash script would do too. Thanks, luis

3 2

converting cache.th13.abs.sig.cluster.mgh into a binary mask
by Erik Lindberg 22 Jan '16

22 Jan '16

Dear Freesurfers, I like to convert a cache.th13.abs.sig.cluster.mgh into a binary mask - so that everything that is below 0.05 will be included in the mask - how can I do this? Eric

2 1

mkanalysis-sess
by Thục Trinh 22 Jan '16

22 Jan '16

Hello, I am using mkanalysis-sess command to configure analysis and I have some questions. 1, After run preproc-sess on raw data, why would we want to repeat all the flag using for preprocessing at mkanalysis-sess (-stc up -fwhm 5). Is it gonna effect to our f.nii if I input different value from the previous preproc-sess command ? 2. -refeventdur: I read that if we have different duration of stimuli, we can set the -refeventdur equal the mean of all stimuli durations. But in my study, the duration of stimulus depends on the reaction time of subject, so it's gonna be different for each subject. how can I manage that? Thank you, Trinh

2 1

surf mm coordinates do not match the individual anatomy
by Julia Berezutskaya 22 Jan '16

22 Jan '16

Hi all, I am loading a subject's surf (lh.pial) into MATLAB using read_surf(). At the same time I have a mesh based on the original subject's anatomy in .nii. The mm coordinates of these two do not match. Does anyone know why? The same anatomy was used for surface reconstruction. The very ranges of vertex coordinates differ by 10-20 mm, and simple translation of coordinates along each dimension does not solve it. Most difference is along Z axis. I understand, that along X axis it can be expected since there is only left hemisphere in surf and both in volume anatomy, but is there a way to coregister the other two dimensions? Thank you, Sincerely, Julia Berezutskaya

2 1

transform statistical map in MNI to surface
by John Anderson 22 Jan '16

22 Jan '16

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