Re: [Freesurfer] total brain volume or intra crainal volume as estimated for total brain volume

Hi Doug I have run recon-all -segstats -s subject on all my subjects, but I can not see total brain volume label. Should I use intra cranial volume? Knut J > Date: Mon, 4 Jun 2012 10:09:16 -0400 > From: gr...@nmr.mgh.harvard.edu > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurf

[Freesurfer] correction for multiple comparisons

Dear FreeSurfer experts, I have some questions about corrections for multiple comparisons in FreeSurfer. I have two samples, one consisting of two groups and one consisting of three groups. I do the comparison with the sample of two groups in qdec. Correcting for multiple comparisons, I get a sig

[Freesurfer] p-value of clusters

Dear all, I am running a qdec analysis. When I press "Find clusters and Goto Max", all values of the significant clusters after FDR correcting appear except for the p values of the clusters. Any idea why this is happening and what I can do? Best, Julia _

[Freesurfer] Questions regarding statistical analysis

Dear FS experts I'm completely new to the world of freesurfer and apologize my silly queries. I'm trying to compare GM volume, cortical thickness, and mean curvature of 34 automatically parcellated cortical structures (data from 'aparcstats2table' command) between control and patient groups (N=3

[Freesurfer] repost - large-scale reconstruction errors

Hi, In reconstructing some normal adult MPRAGEs, I've had a couple of different fairly large errors that I haven't been able to fix: (1) In a handful of subjects, more than half of the brain is lost, I think during the skullstripping step (ie, isn't present on the white matter or brainmask volumes

Re: [Freesurfer] 回复: Re: /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory

Thanks for your rapid reply . best! Xiangzhen Kong 发件人： Anastasia Yendiki 发送时间： 2012-06-07 23:19 收件人： Xiangzhen Kong 抄送： freesurfer 主题： Re: [Freesurfer] 回复: Re: /path/to/dmri/dwi_orig_flip.mghdti.bvecs': No such file or directory Hi Xiangzhen - Currently mri_convert does not support extract

Re: [Freesurfer] Creating a label from an .mgh file

Thanks for the reply. Couple of follow up questions. (1) Which "ID" should be used when creating the mask? The "mc-z.abs.th23.sig.cluster.mgh" file contains clusters labeled based on z values (i.e., non-integers such as -3.698970, +2.130768, etc). Is it possible to divide the *.mgh file by itsel

Re: [Freesurfer] missing ROI when using mri_label2vol to transfer ic2.tri

I've put a new version of mri_label2vol at that ftp site. When you run it, add "--offset 1". This will change the segmentations IDs to go from 1-162 instead of 0-161. doug On 06/08/2012 11:30 AM, Leon wrote: > Hi, Douglas > > I checked the data this morning and confirmed that the missing ROI in

Re: [Freesurfer] Using an ROI and not correcting/"fixing" the rest of the image

Thanks for the quick response! I will begin basic processing and will surely have questions about how the sphere.reg file is used/how it applies. Thanks again Anson -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Thursday, June 07, 2012 12:40 PM To: Kair

Re: [Freesurfer] Creating a label from an .mgh file

Sorry, use the "ocn" file, not the cluster file. This should have integer values, one for each cluster. doug On 06/08/2012 01:04 PM, Ilia wrote: > Thanks for the reply. > > Couple of follow up questions. > > (1) Which "ID" should be used when creating the mask? > The "mc-z.abs.th23.sig.cluster.mg

Re: [Freesurfer] Mris_anatomical_stats: smoothing does not work with surface area maps

Hi Juegen, there will be a file called something like cache.th20.abs.y.ocn.dat in the glm output directory. This will be a text file with number of columns equal to the number of significant clusters (after correction) and number of rows equal to the number of subjects. The value will be the av

[Freesurfer] qdec.table.dat

hi doug, i am loading 917 subjects in qdec.i already made qdec.table.dat which consist the list of subjid, age, gender, lh & rh thickness.. for some reason, it is only displaying the first subject.others are not been detected by qdec. i also looked into tutorial and compared th

Re: [Freesurfer] correction for multiple comparisons

they are two different correction schemes. If they gave the same answer, then it would not make sense to have both. the monte carlo tries to compute the probability of a cluster of the given size under the null hypothesis. FDR controls for the number of false positives relative to the total num

Re: [Freesurfer] repost - large-scale reconstruction errors

Hi Nicole If you upload some examples we will take a look. What version as you running? Have you checked the accuracy of the talairach.xfm? Cheers Bruce On Jun 8, 2012, at 11:19 AM, Nicole Senecal wrote: > Hi, > > In reconstructing some normal adult MPRAGEs, I've had a couple of different