[Freesurfer] Regression coefficient qdec

Dear Freesurfers, I am trying to display the regional regresssion coefficent for age in qdec. However the colorbar still gives me the traditional 0, 1.3 etc is there anyway to change the colorbar. I would like to be able to display only regions that have more than say 0.3 correlation with age - s

[Freesurfer] smoothing

Dear freesufers, I quick question about smoothing of data in cortical thickness analysis. I have a comparison that is rather borderline significant. When using smoothing of 10 mm I get a limited region in the frontal lobe that is differs between groups. Changing to 15 mm I get larger regions - and

[Freesurfer] Doss/Dods

Dear Freesufers, I am currently running mri_glmfit using a relatively simple design: Two groups and one covariate. Design is: 1 -1 0 0 .. to control for the co-variate (age). It is the example with two groups and one covariate in your web-page http://freesurfer.net/fswiki/Fsgdf2G1V I was under t

[Freesurfer] Did not find any volume geometry information in the surface

Hi, I am running mri_glmfit followed by mri_glmfit-sim running the left hemisphere everything works perfect all the way to the visualization in freeview - then I just chift the command to rh instead - running exactly the same command and when I am opening my results in freeview everything gets ye

[Freesurfer] dividing Freesufer subfields into one anterior, middle and posterior region

Dear FS experts. I want to divid the FS subfield segementation into a anterior part, one middle part and posterior segment - or potentially divide the rang into 10% of the whole rang - and then move backword until I extracted 10 subparts. Is there some way I can do that? Thanks Erik _

[Freesurfer] Optimal combination of MRI-sequences

Dear Freesufer experts, We are in the process of starting a large MRI project on normal aging and dementia. There has been a lot of discussions about what sequences to use. We are now thinking about combining several sequences. Is there an optimal combination of MRI sequences for Freesufer

[Freesurfer] Demean Covariates Qdec

Dear Doug and Freesurfers, I noticed that the DOSS option no longer exists in qdec and that Doug said there was a bug related to it. If i want to assess the differences in cortical thickness between groups while covariating for age and gender, since i don't expect any interactions, can i just demea

[Freesurfer] Demean covariate

Dear Doug and Freesurfers, I noticed that the DOSS option no longer exists in qdec and that Doug said there was a bug related to it. If i want to assess the differences in cortical thickness between groups while covariating for age and gender, since i don't expect any interactions, can i just demea

[Freesurfer] Freesurfer versions

Dear Freesurfer experts, I am attaching a document showing the segmentation of a brain in version 5.1 and 5.3 with and without a 3-T flag. Image is from a 3-T camera. What I am wondering about is that it seems that the cortex is too thin in the later version of Freesurfer (both when using 3T

[Freesurfer] Segmentation/cortical thickness

Dear FS expersts! I have two questions: 1) I am looking at the output from a FS run. When looking at the red and yellow lines it appears as the cortical thickness has bin estimated too thin. But when I take away the two lines and just look at the segmentation it looks quite god (and much thicker

[Freesurfer] How to combine attached commands into one run

Dear Freesufers, I want to use the following commands in my recon-all to try to improve my output some difficult images: -gentle to mri_normalize and -min_border_white 85 -min_gray_at_white_border 80 So far I only managed to do this by making one step at a time. I was wondering if there is a

[Freesurfer] Combining FS commands

Dear Freesufers, I want to run: mri_normalize gentle, And mris_make_surfaces min_border_white 85 -min_gray_at_white_border 80 In as few steps as possible as I will run around 800 images. So far I only managed to this by braking up the process several subparts (like doing autorecon1 before m

[Freesurfer] combining FS commands

Dear Freesurfers, I want to run: mri_normalize gentle, And mris_make_surfaces min_border_white 85 -min_gray_at_white_border 80 in MY recon-all script. I understand that I have to put the flag -expert to do this - but I seem to make errors in my command It would be greatly apprecia

[Freesurfer] Can -min_border_white and -min_gray_at_white_border be edited for single subject in a large group of subjects?

Dear Freesufers, I am trying to understand what happens if I go in and edit the numbers for -min_border_white -min_gray_at_white_border in a single subjects in a large group. Generally we aim to set everything identical when running a group of subjects in FS. I went in and had a look at the re

[Freesurfer] Other things to consider when setting -min_border_white -min_gray_at_white_border?

Dear Bruce and Freesufers, Adding to our previous discussion. You managed to fix a very bad segmentation by setting some expert options (mri_normalize -gentle and setting a fixed level for -min_border_white -min_gray_at_white_border). It was a very nice recovery of, what I thought to be, a hopel

[Freesurfer] interaction in glm

Dear Freesurfer experts, I know this has been an ongoing topic in the mailing list – however I would like to raise the issue one more time. In the choice between doss and dods – I usually check if there is a significant interaction and if so my choice is dods. As I understand it you do not recomm

[Freesurfer] MatrixReadTxT: could not scan value [1][1], ERROR: loading C AAA.mtx

Dear Freesufer experts, I have trouble loading a contrast matrix - however I am not sure if something is going wrong earlier ... and this is causing this problem. Below is the error messages that I get plus the contrast matrix and the .fsgd file I am trying to run. I checked this previous mesage

[Freesurfer] Regressing out various categorical variables

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_A

[Freesurfer] converting cache.th13.abs.sig.cluster.mgh into a binary mask

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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mai

[Freesurfer] (no subject)

I just want to run plane correlation with the csf-variable best Eric ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person

[Freesurfer] (no subject)

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: > D

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

Dear Douglas and Freesufers, You suggested: mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05) I tried this and was expecting that I would get a three-dimensional mask in which the statistical significant part would be white and the rest black. This seems not t

Re: [Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

Dear Bruce and Freesurfers, I probably then go about this in the wrong way. My aim is to create a binary mask for regions that I found differences in - in a group-comparison. I then want to export the mask so I can use it as seed area in an fMRI analysis. Can this be done Thanks Eric Hi Er

[Freesurfer] Re mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05)

Dear Bruce and Freesufers, I tried to run the command and then to load it as an overlay - however I get nothing on the surface of the fsaverage brain. The program is telling me that it is including x-number of voxels into the mask but when I check I see nothing on the surface. What is going wro

[Freesurfer] Re mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05 {Disarmed}

Dear Bruce and Freesufers, I get the following message: surfer: Interpreting overlay volume /media/EHD/ALLA_FREESUFER_PROCESSING_TIDIS_NOMAS_AD/qdec/lh.kvot_gender.glmdir/Gend/thresholded.mgh as encoded scalar volume. the two volumes I tried to convert: 1) Volume information for sig.mgh

[Freesurfer] mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh

Dear Bruce and Freesurfer, Yes, that is what I am saying! This what appears in the commandprompt when running the command: input cache.th13.abs.sig.cluster.mgh frame 0 nErode3d 0 nErode2d 0 output thresholded.mgh Binarizing based on threshold min1.3 max+infinity

[Freesurfer] z-scores versus raw_age for correction in GLM_FIT or qdec

Dear Douglas, attached you´ll find the two y.fsgd file from the analysis run in GLM_FIT. the results are completely different (the z-score converted age produces a believable result, while the result correcting with raw age scores seems completely wrong. best regards Olof y.fsgd_raw_age Descrip

[Freesurfer] Creating an illustration on what Freesurfer has considered to be intracranial volume

Dear Freesurfer experts, I would like to create an image on tissue that Freesurfer has been included into the intracranial volume calculation. Is there anyway to summarize segmentations masks so I get one mask containing all tissue that has been included into the intracranial volume? best Erik __

[Freesurfer] Contrast matrix regressing out effect of diagnosis and age

Dear Freesurfer experts, I am running a GLM-model in which I have 6 classes (diagnosis) and two covariates age and variable X). I want to look at mean correlation of variable X. My contrast matrix is as follows: 0 0 0 0 0 0 0 0 0 0 0 0 0.17 0.17 0.17 0.17 0.17 0.17 0.17 (approx. 1/6) Did I get

[Freesurfer] Hippocampal sufields

Dear Freesurfer experts, I am currently running your new pipeline for hippocampal subfield segmentation. However the resolution on my MRI images is too bad for identifying specific cellular layers such as stratum moleculare. My preferred option would be not to divide the different subfields into

[Freesurfer] Running multiple variables in mri_glmfit

External Email - Use Caution Dear Freesurfer experts, I am in the processing of running correlation with cortical thickness for almost 500 CSF variables. Thus I would like to use some sort of script. I previously used the common steps (mri_preproc, mri_glmfit and mri_glmfit-sim)

[Freesurfer] Postdoctoral position in multimodal neuroimaging on frontotemporal dementia

External Email - Use Caution Dear all, We are looking for a post-doc student for our lab at Karolinska institute in Stockholm. We are doing structural and functional MRI research on dementia. In current project we are acquiring multimodal MRI on frontotemporal dementia patients.

[Freesurfer] Post-doc position for MRI-research on frontotemporal dementia available at Karolinska institute.

External Email - Use Caution Post-doc position for MRI-research on frontotemporal dementia available at Karolinska institute. We are looking for a Post-doc researcher for a 1-year scholarship (with a possibility for an extension to 2-year) at our section at the NVS-department at K

[Freesurfer] (no subject)

External Email - Use Caution Post-doc position for MRI-research on dementia and normal aging available at Karolinska institute. We are looking for a Post-doc researcher for a 1-year scholarship (with a possibility for an extension to 2-year) at our section at the NVS-department at

[Freesurfer] Post-doc position in fMRI research available at karolinska institute

External Email - Use Caution Hi we are looking for a new post-doc in neuroimaging at Karolinska Institutet at the Department of NVS. The Department of Neurobiology, Care Sciences and Society (NVS) conducts world leading research in aging, dementia, epidemiology and care sciences.

[Freesurfer] Volume-defined roi

External Email - Use Caution Hi I am reading your tutorial about how to extract Cortical Thickness of a volume-defined ROI Wonder if there is a script that would run these steps in a bach particularly the steps that needs to be done on each individual subjects: map subject thic

[Freesurfer] segmentHA_T1.sh

External Email - Use Caution Hi, I am trying to run the segmentHA_T1.sh with the suffix CA but I seem not be able to write the call correctly How should I call this? best Olof ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu h