[Freesurfer] FDR versus mri_glmfit-sim with --cache option

Dear FS team, I am doing a cortical thickness study using QDEC. I used FDR and got the following clusters: Generating cluster stats using min threshold of 3.8... Found 2 clusters Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX

Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option

Hi Doug, Many thanks for your prompt response and your help. I have one more question please. I searched for mri_surfcluster command and I am not sure what should be my input file. Can you please clarify this for me? Should this be  L-frontal.fsgd since I have more subjects? Thank you. Antonel

Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option

From: Douglas N Greve To: Antonella Kis ; "Freesurfer@nmr.mgh.harvard.edu" Sent: Wednesday, July 18, 2012 12:03 PM Subject: Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option It should be the sig.mgh file in your contrast directory. doug ps. Please post to th

[Freesurfer] p-val from FDR

Hi Doug, You mentioned that in my case when  FDR found a voxel-wise threshold of 3.8  means   p<1.5849e-04. How exactly I you got this p-val? How I can get myp-vals for clusters after FDR? Many thanks. Antonella ___ Freesurfer mailing list Freesurf

Re: [Freesurfer] p-val from FDR

: freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 18, 2012 1:24 PM Subject: Re: [Freesurfer] p-val from FDR 3.8 = -log10(1.5849e-04) On 07/18/2012 12:36 PM, Antonella Kis wrote: > Hi Doug, > > You mentioned that in my case when  FDR found a voxel-wise threshold > of 3.8  means 

[Freesurfer] Converting labels to individual volumetric masks

Dear All, I want  to use cingulate bundle as ROIs more exactly mask  for fiber tracking. Can I use different aseg than the one from Freesurfer for examples can I use segmentation from JHU-WhiteMatter-labels-1mm.nii.gz and their labels JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingula

[Freesurfer] How to converting labels to individual volumetric masks (Repost)

Dear All, I want  to use cingulate bundle as ROIs more exactly mask  for fiber tracking. Can I use different aseg than the one from Freesurfer for examples can I use segmentation from JHU-WhiteMatter-labels-1mm.nii.gz and their labels JHU-WhiteMatter-labels-1mm.txt to get a mask of my cing

[Freesurfer] Question regarding Volumetric masks

Dear All, I want  to use cingulate bundle as ROIs more exactly mask  for fiber tracking. Can someone explain please how I can use the JHU-WhiteMatter-labels-1mm.nii.gz and their labels JHU-WhiteMatter-labels-1mm.txt to get a mask of my cingulate bundle in my diffusion space for each indivi

Re: [Freesurfer] Question regarding Volumetric masks

. You need a registration between the JHU atlas and the individual. The people who developed the JHU atlas can probably tell you how to do this. doug On 07/27/2012 10:39 AM, Antonella Kis wrote: > > > > Dear All, > > I want to use cingulate bundle as ROIs more exactly mask for

[Freesurfer] QDEC's clusters and connectivity maps

Dear FS team, I am trying to find what is the  connection between white matter tracts with reduced FA and a number of cortical regions/clusters with significant reduction in cortical thickness from QDEC. Is there a way to overlap my cortical regions with reduced thickness more exactly the clus

[Freesurfer] Convert QDEC clusters on the MNI_152_T1 space

Dear All, Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain template? Thank you. Antonella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

[Freesurfer] Fw: Convert QDEC clusters on the MNI_152_T1 space

freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, August 21, 2012 4:55 PM Subject: Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat doug On 08/21/2012 11:06 AM, Antonella Kis wrote: > Dear All, > > Is possible to overl

[Freesurfer] How to Convert QDEC clusters to standard MNI_152_T1 space

/average/mni152.register.dat doug On 08/21/2012 11:06 AM, Antonella Kis wrote: > Dear All, > > Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain > template? > > Thank you. > Antonella > > > ___ > Freesurfer maili

[Freesurfer] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space

Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat doug On 08/21/2012 11:06 AM, Antonella Kis wrote: > Dear All, > > Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain > template?

[Freesurfer] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space

PM Subject: Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat doug On 08/21/2012 11:06 AM, Antonella Kis wrote: > Dear All, > > Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain &

Re: [Freesurfer] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space

e, it would be fsaverage). Leave fillthresh at 0; the clusters cannot overlap. doug On 8/27/12 4:17 PM, Antonella Kis wrote: > > > > > > Hi, > > I want to overlay  my QDEC clusters on the connectivity maps in FSL  on the MNI ( this is the

[Freesurfer] Error with annot file

Hi, I am trying to run the mri_label2vol but I am getting the following error. I am not sure which annot file I should use for my QDEC clusters. I tried to use my annot file from mri_glmfit-sim but it didn't work. I was running: mri_label2vol --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURF

[Freesurfer] Repost: Error with annot file

Hi, I am trying to run the mri_label2vol but I am getting the following error. I am not sure which annot file I should use for my QDEC clusters. I tried to use my annot file from mri_glmfit-sim but it didn't work. I was running: mri_label2vol --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESU

[Freesurfer] Average Thickness in QDEC

Dear Experts, What is the best way to get the average thickness for each subject in QDEC, more exactly for the uncorrected clusters? I know when running QDEC theer is a stats_tables file saved so I wonder if the lh. aparc.thickness.stas.dat represents the mean cortical thickness. Should this va

[Freesurfer] hippocampal subfield segmentation

Dear FS team, I would like to know if there is any options to get the hippocampal subfield segmentation so I can get the volume for each segmentation if I was running only recon-all for all my subjects or I need to re-run recon-all but with a hippocampal subfield segmentation option this tim

[Freesurfer] Head, body and tail of hippocampus

Dear FS team, I would like to know which subfield ( left_presubiculum,   left_CA1,   left_CA2-3,   left_fimbria,   left_subiculum,   left_CA4-DG,   left_hippocampal_fissure) contribute to the head, body and  tail of left  hippocampus. It also seems that the first column of nonPartialVolumeStat

[Freesurfer] Hippocampus volume

Dear FS team, After I ran the recon-all to get the total cortical thickness, the volume  of the left hypocampus ( = the number of voxels) equals to 2166 which I thought should be the total hippocampal volume. But if we add all the voxel numbers from the hippocampal subfield I will get a much large

[Freesurfer] dcm conversion

x27;s studies? Sorry for this silly question but for all my other subjects I had only one file .nii.gz and I have no clue from where is coming. Thank you very much. Antonella From: Bruce Fischl To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu"

[Freesurfer] Pre-processing issues

Dear Bruce, I have two more questions for today, please: 1). Just to be sure that  I understood correct: for my  cortical thickness studies and also for a group studies analysis I will use only the data from the 3DAx_T1series which was converted to a .nii.gz file. Is this right? 2). If I want

Re: [Freesurfer] Pre-processing issues

labelling are correct? Thank you very much. Antonella From: Bruce Fischl To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Friday, July 22, 2011 3:47 PM Subject: Re: [Freesurfer] Pre-processing issues Hi Antonella do you know what t

[Freesurfer] Unknown label

Hi Bruce, I forgot to ask why my data does not include an  unknown region in my aparc.stats file? My stats  data starts with bankssts region and continue with caudalanteriorcingulate, etc. Do I need to have the unknown region if I use the new version of the FS 5.1.0? Thank you. Antonella _

[Freesurfer] Loading atlases

Hi, I would like to check if my subcortical segmentation is correct so I was running: tkmedit SUBJECT1 brainmask.mgz \     -aux T1.mgz -surfs \     -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt 1).  Pial (red line), and white (yellow line) surfaces are shown and I wonde

[Freesurfer] Corrections for the Pial surface

Hi Bruce, Thank again for your advice. I am not sure about the data collection but I will find out soon. In the mean time I have two more questions: 1). The FS tutorial shows for the surface outlines  (by loading the -surfs) three line: the yellow indicating the white surface, the red for the pi

[Freesurfer] "orig surface" button

I can see the same point that I choose in one view for example the coronal view in another view example horizontal view? How I can select this point in one view and make it visible in another view? Thanks, Antonella From: Bruce Fischl To: Antonella Kis Cc: &

Re: [Freesurfer] "orig surface" button

nella From: Bruce Fischl To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, July 28, 2011 11:15 AM Subject: Re: "orig surface" button Hi Antonella, if it's not active then it probably failed loading the orig surface. Can

[Freesurfer] Intensity Normalization error

Dear Bruce, 1). What is the minimum value/the range for the intensity in order to be considered acceptable? I know the value in wm should be very close to 110 but what is the accepted value closed to this? If is not exactly 110 (foe example if is 101) do I need to add control points in order to

[Freesurfer] Error with aparcstats2table

Hello everyone,  I was trying to create a table with my statistical results (the cortical thickness and the number of vertices) and I was running: aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t lh.aparcstas.THICKNESS.txt  When I tried to also get the number of vertices

[Freesurfer] Error with aparcstats2table

Hi,  I was trying to create a table with my statistical results (the cortical thickness and the number of vertices) and I was running: aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t lh.aparcstas.THICKNESS.txt  When I tried to also get the number of vertices a table by

Re: [Freesurfer] Error with aparcstats2table

: Bruce Fischl To: Antonella Kis Sent: Friday, July 29, 2011 5:24 PM Subject: Re: [Freesurfer] Error with aparcstats2table doug and nick can help with that On Fri, 29 Jul 2011, Antonella Kis wrote: > Hi Bruce, > > Thanks again for helping. I mean in the aparc stats I have for each >

[Freesurfer] RE;Corrections with the oPTIC NERVE

Hi Bruce, Many thanks for your answer and for your valuable help. I was just following the the examples from the Free Surfer manual on the page 57 (please see the attachment). I believe my image (the slice I sent you on yesterday) is similar or closed looking with the one on the page 57. Since

[Freesurfer] Which hemisphere is in the sagital view of the wm

Hi, When visualizing the wm.mgz in the coronal view we can see both hemispheres: lh and rh. How do I know which hemisphere I am visualising in a sagittal view?  Do I have a transition from lh to the rh while passing through the slices? Thank you, Antonella _

[Freesurfer] FSGDF matrix

Dear Bruce, I am ready to start my GLM group analysis. I am trying to construct the FSGDF by constructing an my_age_fsgd.txt file.  I was reading the tutorial and I am not sure if I need to put together my patients and controls in my FSGDF since my group study will be for patients versus contro

Re: [Freesurfer] FSGDF matrix

talairach.m3z. What is the difference between this two and what should I choose or how I know which one I have to choose? Thank you very much for your help. Antonella From: Bruce Fischl To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent:

[Freesurfer] (no subject)

Dear Freesurfers, I am ready to run the make_average_subject and I need to specify   -xform  for the talairach transform: talairach.lta , talairach.m3z or talairach.xfm. What is the difference between this and what should I use for the make_average_subject in order to prepare my data for the GLM

[Freesurfer] make_average_subject

talairach.m3z? Many thanks. Antonella From: Bruce Fischl To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, August 11, 2011 12:52 PM Subject: Re: [Freesurfer] (no subject) Hi Antonella talairach.lta and .xfm are linear trans

[Freesurfer] Error with mri_preproc

Dear freesurfers, I am trying to see what are the group differences in cortical thickness of patients with right and left FLE compared to controls using the GLM. I created a txt file in gedit called my_age_fsgd.txt (please see the attachment) containing my subjects (patients and controls) and

[Freesurfer] thickness-age correlation

Dear Freesurfer experts, I am doing a thickness-age correlation group difference study (patients versus controls. I would like to know if: 1) my contrast vector defined as 0 0 0.5 0.5 is correct in order to test the change in thickness with age 2)what is the best iteration number for the simul

Re: [Freesurfer] mri_glmfit-sim

e my treshold until I find some activation? Thank you very much for your valuable help. Antonella From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Tuesday, August 16, 2011 12:04 PM Subject: Re: [Freesurfer] thickne

Re: [Freesurfer] mri_glmfit-sim

his mean a low activation? If yes, what I have to do? Thank you very much! Antonella From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Wednesday, August 17, 2011 11:53 AM Subject: Re: [Freesurfer] mri_glmfit-sim

Re: [Freesurfer] mri_glmfit-sim

iteration if I run this part? Do I need to add this and  do I need to mention the threshold in the above coding? THANKS! Antonella From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Wednesday, August 17, 2011 1:10 PM S

Re: [Freesurfer] mri_glmfit-sim

! Antonella From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Wednesday, August 17, 2011 2:55 PM Subject: Re: [Freesurfer] mri_glmfit-sim for the cache, the simulation has already been done (using 10,000). This makes it m

[Freesurfer] Error loading annot file

lh.age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot How can I fix this error? THANKS! Antonella From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Wednesday, August 17, 2011 2:55 PM Subject: Re: [Freesurfer] mri_

Re: [Freesurfer] mri_glmfit-sim

From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Wednesday, August 17, 2011 1:10 PM Subject: Re: [Freesurfer] mri_glmfit-sim Antonella Kis wrote: > Hi Doug, > > > Thanks again for your help. There are few more things no

[Freesurfer] Avg.Thickness in a cluster

Dear Doug, I just checked my results for the  average thickness from each subject generated in the csdbase.y.ocn.dat file in different clusters (e.g.  I have 5 clusters for p<0.05). For cluster #1 - posteriorcingulate,  the average thickness for subject 1 is different from the average thic

Re: [Freesurfer] mri_glmfit-sim

From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, August 18, 2011 1:09 PM Subject: Re: [Freesurfer] mri_glmfit-sim No you don't. This is the reason I wrote mri_glmfit-sim -- so you don't need to

[Freesurfer] GLM or Qdec ?

Dear FS experts, I finished running the GLM and I wonder what is the best way to further analyse my data in order to see if there is any relation between age (at seizure onset) and cortical thickness for my  patients versus control group. 1).  Why when I overlay the sig.mgh in tksurfer lh infla

[Freesurfer] GLM or Qdec

Dear FS experts, I finished running the GLM and I wonder what is the best way to further analyse my data in order to see if there is any relation between age (at seizure onset) and cortical thickness for my  patients versus control group. 1).  Why when I overlay the sig.mgh in tksurfer lh inf

[Freesurfer] correction for multiple comparisons

So to run for multiple corrections in fact I will need to run: mri_glmfit-sim \ --glmdir rh.age.glmdir \ --cache 2 neg \ --cwpvalthresh .025 --overwrite Please advise me. Thank you for your time and help. Antonella From: Douglas N Greve To: Antonella K

Re: [Freesurfer] correction for multiple comparisons

right? Please advise. Thank you. Antonella From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Tuesday, August 23, 2011 4:33 PM Subject: Re: [Freesurfer] correction for multiple comparisons Yes, that is correct, you sh

[Freesurfer] fsaverage

Dear All: I wonder if for a  new FSGD file (e.g. age.fsgd) the resample of each subjects data to fsaverage (into a common space), as well as concatenating all the subjects' into a single file, will change my old  fsaverage.  Thank you. Antonella ___ F

[Freesurfer] Fw: fsaverage

. Antonella From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Tuesday, August 23, 2011 4:33 PM Subject: Re: [Freesurfer] correction for multiple comparisons Yes, that is correct, you should use .025 if you are correcting

Re: [Freesurfer] Multiple corrections

Hi Doug, Many thanks for your valuable answer. Can you please briefly explain some other issues: 1). what exactly means Correction for Multiple Comparisons and how this is done when using --sim method with --cache. 2). do I need to do an estimation  FDRthresholding in tksurfer for GLM meth

Re: [Freesurfer] Fw: fsaverage

elp. Antonella From: Douglas N Greve To: Bruce Fischl Cc: Antonella Kis ; "freesurfer@nmr.mgh.harvard.edu" Sent: Thursday, August 25, 2011 12:23 PM Subject: Re: [Freesurfer] Fw: fsaverage That "2" is a voxel-wise threshold used to form the

[Freesurfer] DTI and Fresurfer

Dear All, I would like to do DTI analysis on my subjects data. I finished the pre-processing using recon-all and also I used GLm for the group study. Can you please let me know how I can do DTI analysis using FSL in Freesurfer? What steps I need to follow? Many thanks, Antonella __

[Freesurfer] DTI and FS

Dear FS experts, I'm interested in doing DTI analysis, using FS. Do I need to have functional data (feat) and then do I need to register the anatomical data on the functional one? My MRI data contains the following folders: 3DAx_T1, Ax_Flair, Ax_T2PD, DTI_15, DTI_30. I am not sure for a DTI /FS

[Freesurfer] Error with dt_recon

Dear All: I am running the dt_recon:# setenv FREESURFER_HOME /usr/local/freesurfer    # setenv SUBJECTS_DIR $FREESURFER_HOME # cd /usr/local/freesurfer/NPI001 # dt_recon --i /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm --s /usr/local/freesur

[Freesurfer] Fw: Error with dt_recon

Dear Bruce: I am running the dt_recon:# setenv FREESURFER_HOME /usr/local/freesurfer    # setenv SUBJECTS_DIR $FREESURFER_HOME # cd /usr/local/freesurfer/NPI001 # dt_recon --i /usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm --s /usr/local/fr

[Freesurfer] File correction during NIFTI conversion

Dear FS experts, While doing a NIFTI conversion for my dicom files I tried near mri_convert the MRIcron conversion. I saw that during this conversion the MRIcron is doing a correction and image orientation such that one of my final NIFTI file is having a  smaller size that the NIFTI file coming

[Freesurfer] mri_glmfit simulator

Dear Doug, Can you please give me some details about how the corrections by multiple comparisons are done? Which step in the following code is doing the corrections? Are the corrections for multiple comparisons done by cache or by cwpvalthresh or the corrections are done by some parts that are

[Freesurfer] Colours for significant clusters

Hi, Based on Group Analysis tutorial by loading the cluster annotation in tksurfer you can visualize  all clusters, regardless of significance. Then  changing the  label mode to "Outline" by hitting the outline button and  loading the cluster p-value overlay I can see all the significant cluste

[Freesurfer] Cortical Thickness in significant clusters

Dear Doug, I know as you told me in past that the average value for the cortical thickness in significant clusters is given in the cache.th20.neg.y.ocn.dat file under lh-Avg-thickness-age-Cor file. 1).Is there another way to get the cortical thickness for the significant clusters, other than

[Freesurfer] Group Analysis

Dear All, When I designed the  matrix consisted of two discrete groups, (patients vs. controls), I choose age as a covariate so during my analysis I was  lookingif there is a difference in the  cortical thickness within patients versus controls while accounting for age. Should I change my FSGD i

[Freesurfer] Group Analysis

Dear All, When I designed the  matrix consisted of two discrete groups, (patients vs. controls), I choose age as a covariate so during my analysis I was  lookingif there is a difference in the  cortical thickness within patients versus controls while accounting for age. Should I change my

[Freesurfer] Contrast Vector while eliminating age and gender

Dear All, What should be my contrast vector if I want to do a direct comparison between groups (patients vs. controls) after eliminating gender and age? Should this be [1 -1]? Should I change my FSGD in order to be able to compare between patients and controls accounting for age (I want t

[Freesurfer] Discrete and Continuous factors in QDEC

Hi Doug, One more question please: if I want to do a cortical thickness study between two groups (patients and controls) and I want to eliminate the age and gender what should be my Discrete and Continuous factors in QDEC? Thank you. AK ___ Freesurf

[Freesurfer] QDEC and Cortical Thickenss

possible to get more clusters after running FDR in comparison with the no. of clusters when I set up the thresh 2? Thank you very much and have a great weekend! Antonella From: Douglas N Greve To: Antonella Kis ; freesurfer Sent: Thursday, September 22, 2011 3:53

[Freesurfer] QDEC stats table output

Hi, After running QDEC, I would like to  output in a table the thickness values within each clusters. I know this is a dependent variable and I can see the values on the plot but is there a way that I can get this values in a table? Thanks, Antonella From:

[Freesurfer] QDEC stats table output

Hi, After running QDEC, I would like to  output in a table the average value for the cortical thickness within each clusters. I know this is a dependent variable and I can see the values on the plot but is there a way that I can get this values in a table ? Thanks, Antonella___

Re: [Freesurfer] QDEC stats table output

clusters? Many thanks, Antonella From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Monday, September 26, 2011 10:23 AM Subject: Re: [Freesurfer] QDEC stats table output Will this work (this is from running mri_

[Freesurfer] QDEC stats table output

of the clusters? Many thanks, Antonella From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Monday, September 26, 2011 10:23 AM Subject: Re: [Freesurfer] QDEC stats table output Will this work (this is from running

Re: [Freesurfer] QDEC stats table output

k you very much for your help. Antonella From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Monday, September 26, 2011 11:19 AM Subject: Re: [Freesurfer] QDEC stats table output You can run mri_glmfit-sim on the QDEC o

[Freesurfer] Fw: QDEC stats table output

k you very much for your help. Antonella From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Monday, September 26, 2011 11:19 AM Subject: Re: [Freesurfer] QDEC stats table output You can run mri_glmfit-sim on

[Freesurfer] Clusters formation by FDR

Good morning Doug, I will really appreciate if you can give me an advise on how I can get the mean average of the cortical thickness value for the FDR clusters so before Monte Carlo Simulation. Many thanks, Antonella___ Freesurfer mailing list Freesu

[Freesurfer] Error with mri_glmfit-sim

Good morning Doug, I tried running the -sim on my QDEC output (as you recommended me last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do

[Freesurfer] Error with mri_glmfit-sim

Good afternoon, I tried running the -sim on my QDEC output (as  recommended last days) but for some data the FDR gives me error (cannot calculate clusters statistics) so mri_glmfit-sim is not working either since the corrections by multiple comparisons is not working. What should I do in t

[Freesurfer] Error with Clusters Summary (ASAP)

Dear Doug, Sorry, I am coming up with the same problem. I am running the mri_glmfit_sim on the QDEC results to get the text file with the cortical thickness average and cluster summary but unfortunately I see for one side the --sim is not give me any clusters even if I can see 5 in QDEC after c

[Freesurfer] Error with Clusters Summary

Hi, Sorry, I am coming up with the same problem. I am running the mri_glmfit_sim on the QDEC results to get the text file with the cortical thickness average and cluster summary but unfortunately I see for one side the --sim is not give me any clusters even if I can see 5 in QDEC after ch

[Freesurfer] Error for Patients Abnormal Side Right

Dear Doug, Seems that this will never end...It is so painful already. I was running the --sim as you told me and it worked out for my Sample data formed by controls and patients with Abnormal side Left. Now, I am doing the same thing but I am getting an error for both lh and rh. Here is what I

[Freesurfer] Error for Patients Abnormal Side Right

Hi Doug, Seems that this will never end... I was running the --sim as you told me and it worked out for my Sample data formed by controls and patients with Abnormal side Left. Now, I am doing the same thing but I am getting an error for both lh and rh. Here is what I was running: mri_glmfit

[Freesurfer] Error due to fwhm (ASAP please)

Hi Doug, I believe I got the error for the Abnormal Side R because the fwhm for the clusters with thresh 2 in QDEC is fwhm = 31.843147 as you can see below: and when I run mri_glmfit-sim it gives me the error: and when I run mri_glmfit-sim it gives me the error that cannot find fwhm 32: ERROR

[Freesurfer] Error due to fwhm

Hi, When I ran the QDEC on patients with abnormal side right, the fwhm for the clusters at thresh 2 is fwhm = 31.843147. Then, I ran mri_glmfit-sim on the QDEC output and it gives me the following  error (cannot find fwhm 32): ERROR: cannot find /usr/local/freesurfer/average/mult-comp-cor/fs

Re: [Freesurfer] Error due to fwhm

advise. Thank you. AK From: Douglas N Greve To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" ; "fis...@nmr.mgh.harvard.edu" Sent: Friday, September 30, 2011 10:52 AM Subject: Re: Error due to fwhm That exceeds the valued for which the tab

[Freesurfer] Default for fwhm while running mri_glmfit

  the default in FS while running the mri_gmlfit (mri_surfcluster? What if my data was smoothed at 10 while running the mris_preproc --cache-in thickness.fwhm20.fsaverage \ Please advise. Thank you. AK From: Douglas N Greve To: Antonella Kis Cc: "frees

[Freesurfer] Default for fwhm while running mri_glmfit

- Forwarded Message - From: Antonella Kis To: Douglas N Greve Sent: Friday, September 30, 2011 12:31 PM Subject: Re: [Freesurfer] Default for fwhm while running mri_glmfit I see.I am not sure what exactly you mean by an outlier in my data,but if there will be an outlier, why the

[Freesurfer] cwp and QDEC color scale

Hello Surfers, I would appreciate if you can help me with the following question: what should be the range values on the  QDEC and/or GLM  color scale if the cwp values for the cached clusters at thresh 2 and cwpvalthresh .99 are between 0.4465 and 0.9710? Many thanks. AK__

[Freesurfer] cwp and QDEC color scale

Hello Surfers, I would appreciate if you can help me with the following question: what should be the range values on the  QDEC and/or GLM  color scale if the cwp values for the cached clusters at thresh 2 and cwpvalthresh .99 are between 0.4465 and 0.9710? Many thanks. AK__

[Freesurfer] Resampling NIFTI images

Dear FreeSurfers, I would like to know if there is a way to re-sample a NIFTI image (obtained after MRIcron conversion, from a dcm image) in Freesurfer with a scale factor of 2. I saw about mri_convert but this doesn't give me any option for the scale factor (for e.g. I want to drop each second

[Freesurfer] Resampling NIFTI images

Dear FreeSurfers, This is a question I posted yesterday and I got not answer yet. I am trying to re-sample a NIFTI image (obtained after MRIcron conversion, from a dcm image) in Freesurfer with a scale factor of 2. I know about mri_convert with the option -rt but this doesn't give me any opti

[Freesurfer] cwp and QDEC scale

Hi, I would appreciate if you can help me with the following question: what should be the range values on the  QDEC and/or GLM  color scale if the cwp values for the cached clusters at thresh 2 and cwpvalthresh .99 are between 0.4465 and 0.9710? Also, I wonder if there is a way in QDEC to

[Freesurfer] CVS or MNI registration

Hi Bruce, I will be very grateful if you can give me an advise regarding registration. In TBSS there is recommended if the subjects are  young children (the adult-derived FMRIB58_FA target is inappropriate), to  identify the "most representative" one, and use this as the target image. This target

[Freesurfer] Sag3D_T1 or Axial_T1

Dear Freesurfers, I have a set of MRI data collected in an Axial_T1 and some in Sag3D_T1. I wonder if after dcm to nii conversion when I get a 3D or 4D volume (if further use for FSL) it really matter how my data was acquired (Axial or Sag) since the NIFTI file is in fact a volume. Should I do

[Freesurfer] Sag3D_T1 or Axial_T1

Dear Freesurfers, I have a set of MRI data collected in an Axial_T1 and some in Sag3D_T1. I wonder if after dcm to nii conversion when I get a 3D or 4D volume (if further use for FSL) it really matter how my data was acquired (Axial or Sag) since the NIFTI file is in fact a volume. Should I d

[Freesurfer] DTI Group Analysis Study

Hi, I am trying to do a DTI Group Analysis study using a MNI152 standard space for registration. 1). I wonder in case I want to use MNI 152 and not CVS space using TRACULA if I have to follow all the steps     starting Setting Up a Configuration File to run Tracula and then to  continue

Re: [Freesurfer] DTI Group Analysis Study

results from FSl with th eone from Freesurfer: TRACULA or dt_recon method. Please advise. Many thanks, Antonella From: Anastasia Yendiki To: Antonella Kis Cc: "freesurfer@nmr.mgh.harvard.edu" Sent: Friday, November 11, 2011 4:45 PM Subject: Re: [Frees

[Freesurfer] CVS template for registration

Dear all: Based on the DTI Basic Tutorial I understood that MRI data can be resampled & registered in CVS space (by running  mri_cvs_register), but alternatively can be normalized  in any other (for example, MNI or Talairach). Can you please let me know how this can be done in MNI152 space? Sho

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