Re: [Freesurfer] Regarding_ Midbrain_misalignment

't > know what is going wrong. Try doing the visualization in freeview. Also see > if the amyg/thal seem to be in the right place relative to brainstem when > you visualize all of them together. > > On 6/25/17 9:31 AM, Dr Sampada Sinha wrote: > > Hello Dr Greve, > > Will

Re: [Freesurfer] Regarding_ Midbrain_misalignment

specify the output file as > mdd_brainstem.mni305.nii.gz and it will be saved in nifti. No need for an > additional step > > cheers > Bruce > > > > > On Sun, 25 Jun 2017, Dr Sampada Sinha wrote: > > Hello Dr Greve, >> >> Will you please let me know if the above

Re: [Freesurfer] Regarding_ Midbrain_misalignment

Hello Dr Greve, Will you please let me know if the above said process I did to overlay brainstorm mask on colin atlas is correct? Thanks and regards, Sam On Tue, Jun 20, 2017 at 8:47 PM, Dr Sampada Sinha <drsampadasi...@gmail.com> wrote: > Thanks Dr Douglas for your reply.

Re: [Freesurfer] Regarding_ Midbrain_misalignment

it on the mni_colin_t1hires atlas using mango. Thanks and regards, Sam On Tue, Jun 20, 2017 at 7:59 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > how was it created? > > On 6/20/17 9:41 AM, Dr Sampada Sinha wrote: > > Dear freesurfer experts, > > I am trying to over brainstem

[Freesurfer] Regarding: Comparing hippocampal volume from different scanners for two different population

, May 30, 2017, Douglas Greve <gr...@nmr.mgh.harvard.edu <javascript:_e(%7B%7D,'cvml','gr...@nmr.mgh.harvard.edu');>> wrote: > You do need to take it into account, but you cannot if one group is 1.5T > and the other is 3T. > > > > On 5/28/17 10:41 AM, Dr Sampada Sinha wrot

[Freesurfer] Regarding: Comparing hippocampal volume from different scanners for two different population

in the hippocampal volume correlating with their cognitive scores between the two study groups. Do I need to take into consideration different scanner parameters when doing the statistics? How do I go about it? Thanks for your help. Kind regards, Sam -- Dr Sampada Sinha ​Research medical scientist (B

Re: [Freesurfer] ERROR

Subject directory is defined. Try running export SUBJECTS_DIR=$PWD and then run tkmedit command. That might work. Kind regards, Sam On Mon, Apr 17, 2017 at 8:12 PM, David Semanek wrote: > In my experience, OSX has weird issues with things in system and >

Re: [Freesurfer] Regarding: mris_label2annot

u can also save the annot to another folder (something > like --a ./myaparc to save in the current directory) > > > On 02/03/2017 03:21 AM, Dr Sampada Sinha wrote: > > Dear freesurfer experts, > > > > I am trying to create medial temporal lobe and for that I ran t

Re: [Freesurfer] Fwd: Regarding: mris_label2annot

age directory into your working directory: > > cp -r ${SUBJECTS_DIR}/fsaverage ${YOUR_DIR}/fsaverage > > > Best, > -- > Seung-Goo KIM > > On 2017-02-04, at 03:07, Dr Sampada Sinha <drsampadasi...@gmail.com> > wrote: > > Dear Freesurfer exp

[Freesurfer] Fwd: Regarding: mris_label2annot

Dear Freesurfer experts, I am trying to create medial temporal lobe and for that I ran the command mri_annotation2label to create ?h.entorhinal.label, ?h.temporalpole.label and ?h.parahippocampal.label from fsaverage and stored these labels in labels.?h directory. After this I ran

[Freesurfer] Regarding: mris_label2annot

Dear freesurfer experts, I am trying to create medial temporal lobe and for that I ran the command mri_annotation2label to create ?h.entorhinal.label, ?h.temporalpole.label and ?h.parahippocampal.label from fsaverage and stored these labels in labels.?h directory. After this I ran

[Freesurfer] REPOST: Regarding: Habenula ROI

Dear freesurfer experts, Is it possible to create Habenula as region of interest from fsaverage (orig.mgz images) using tkmedit? I will be using following links to guide me for creating Habenular region of interest. Hope my question is answered since the next question is related to this please.

[Freesurfer] Regarding: Segmentation violation detected (FS version dev6)

Dear freesurfer experts, I am trying to so the brainstem segmentation with freesurfer version *freesurfer-Darwin-OSX-stable-v6-beta-20161116-5037eae. *I incorporated the MCR in the fs dev directory. When I run the command recon-all -s foo -brainstem-structures. I am getting the following error:

[Freesurfer] Regarding: dlPFC volume

Dear freesurfer experts, I managed to create dlPFC ROI and successfully extracted the cortical surface parameters. I also want to have the whole volume of dlPFC (*not* the gray matter volume). Will it make any sense if I multiply dlPFC ROI surface area with its corresponding thickness to get a

[Freesurfer] Regarding: freesurfer vs. Neuroquant

Hello freesurfer experts, Is there any paper comparing the volumetric analysis done by freesurfer and that done by Neuroquant? So far, I have found only one link on Neuroquant topic on freesurfer forum (that says Neuroquant uses only one part of freesurfer). Will appreciate if I can be given more

[Freesurfer] Superimposing average hippocampal colume onto a betted brain

Dear freesurfer experts, Thank you for guiding me on how to create average volume of all subjects of depression patients. I later binarized the average volume generated to extract the amygdala and hippocampus volume(Right and left). Please find attached. How do I superimpose the extracted

Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

y not just take the volume of the hippocampus from the aseg.stats? Why > do you want an mgz? You just want one number per subject, right? > > Bruce > > > > On Tue, 12 Jul 2016, Dr Sampada Sinha wrote: > > Dear Bruce, >> >> Thanks for you for your response. I am trying

Re: [Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

dividual subject data is not resampled to a common > coordinate system, so just averaging them as is won't produce anything > interested. > > cheers > Bruce > > On Sun, 10 Jul 2016, Dr > Sampada Sinha wrote: > > > Dear freesurfer experts, > > Will you please let me

[Freesurfer] Regarding: Concatenating hippocampal to generate sig.mgh

Dear freesurfer experts, Will you please let me know if it's possible to get one average mgz image file by concatenating the hippocampal volumes of different subjects using dev version? Since, I already have the hippocampal subfields mgz volume files, I intend to run the glmfit later on between

[Freesurfer] Regarding: Surface projection of WMHs volume

Dear freesurfer expert, I don't know if this question make any sense but is there a way to project white matter hypointensities volume onto the surface? Thanks and kind regards, Sampada -- Sampada Pre-doctoral student Department of Geriatric Mental Health (DGMH) King George Medical

Re: [Freesurfer] Regarding: oblique view

sorry > Bruce > > On Fri, 8 Apr 2016, Dr Sampada Sinha wrote: > > Hello Bruce, >> >> Thanks for your reply. Brief history of my problem so far is that: as you >> noticed before, my images have very low resolution and very less contrast. >> My images slice thick

Re: [Freesurfer] Regarding: oblique view

to isotropic > > cheers > Bruce > > On Wed, 30 Mar 2016, Dr Sampada Sinha wrote: > > Hello Bruce, >> >> Thanks for following it up. ​Sorry for tardy response. I am at the mercy >> of >> power supply and Internet connectivity here. ​The details of scans are

[Freesurfer] Regarding: Group analysis of WMHs

Dear freeesurfer experts, I am trying to calculate WMHs of MDD patient populations. I ran the T2FLAIR separately after processing T1 with recon-all. Presently, I don't have any dwi data where I can project the WMHs onto the WM tracts. Will you please tell me how do I project the WMHs of 29 MDD

Re: [Freesurfer] Regarding: oblique view

ou have defects that large you should look at the inflated.nofix > surface to see what they are. > > What is your voxel resolution? > > cheers > Bruce > > On Tue, 22 Mar 2016, Dr Sampada Sinha wrote: > > Thanks Bruce for your reply. I did run it thru' recon-all. It went for &

Re: [Freesurfer] Regarding: oblique view

you tried running it through recon-all? It may work fine > On > Tue, 22 Mar 2016, Dr Sampada Sinha wrote: > > > Thanks Bruce for your reply. The acquisition was oblique and the voxel > size doesn't > > conform to the 1mm cube isotropic. I am trying to work on it and fig

Re: [Freesurfer] Regarding: Freesurfer 6.0 dev version

da > > V6 is not out yet, although we are actively (frantically?) working on it. > > cheers > Bruce > On > Tue, 22 Mar 2016, Dr Sampada Sinha wrote: > > > Dear freesurfer experts, > > > > I am trying to do hippocampal subfields segmentation on Mac. I will >

Re: [Freesurfer] Regarding: oblique view

Fischl <fis...@nmr.mgh.harvard.edu> wrote: > what do you mean by "adding" an oblique angle? If you mean acquiring the > data obliquely you should be fine as long as the voxels are close to 1mm > isotropic. > > cheers > Bruce > On Sun, 20 Mar 2016, Dr Sampa

[Freesurfer] Regarding: Freesurfer 6.0 dev version

Dear freesurfer experts, I am trying to do hippocampal subfields segmentation on Mac. I will greatly appreciate if freesurfer 6.0 version link is forwarded to me. With thanks and regards, Sampada Pre-doctoral student KGMU, Lucknow India ___ Freesurfer

[Freesurfer] Regarding: oblique view

Dear freesurfer experts, Does adding an oblique angle during coronal or axial acquisitions of T1w images lead to topographical errors during mri_fix_topology process? Thanks and regards, Sampada -- Sampada Sinha ___ Freesurfer mailing list

[Freesurfer] Regarding: running lgi with freesurfer dev6 and matlab2016a

Dear freesurfer expert Marie, I am trying to run lgi after doing recon-all. I am getting stuck with an error. Just wanted to know if freesurfer dev6 is compatible with newest Malta 2016a version. Thanks and regards, Sampada Predoctoral student KGMU, Lucknow India -- Sampada Sinha

Re: [Freesurfer] Regarding: running lgi with freesurfer dev6 and matlab2016a

Sorry for the typos...its Matlab 2016a version I meant! On Wednesday, March 16, 2016, Dr Sampada Sinha <drsampadasi...@gmail.com> wrote: > Dear freesurfer expert Marie, > > I am trying to run lgi after doing recon-all. I am getting stuck with an > error. Just wanted to know

[Freesurfer] Regarding: T2w and HcV analysis

Dear freesurefr experts, Hope this mail finds you all doing well. I want to calculate hippocampal subfield volume using T2w mages. Is the recon-all command same as we do for the T1images (recon-all -i input to T1.nii.gz -s 001 -all)? I was not able to understand the recon-all command for the T2w

Re: [Freesurfer] Regarding: Brainstem volumetric result

: Dr Sampada Sinha drsampadasi...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, August 12, 2015 3:52:36 PM Subject: [Freesurfer] Regarding: Brainstem volumetric result Dear freesurfer experts, I successfully managed to install and run the freesurfer

[Freesurfer] Regarding: Brainstem volumetric result

Dear freesurfer experts, I successfully managed to install and run the freesurfer dev version6 for brainstem segmentation analysis. But, looking at the result of brainstem volume in brainstemSsVolumes.v10.txt, the whole brainstem volume is 14439.355323 and the brainstem volume by recon-all out

Re: [Freesurfer] QDEC question

Hello Dr Greve, Many thanks for replying to me. We are not including eTIV as a covariate. Since we did not find any correlation with the thickness. Kind regards, Sampada ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Regarding: 3 groups and 1 covariate contrast

Dear freesurfer experts, I am trying to find group difference (thickness) among 3 groups (SCA1, SCA2, SCA3) taking in account one covariate (CAG levels). Will you please let me know if I need to use DODS or DOSS, though I am more interested in using DODS. I read the FSGD examples page (

Re: [Freesurfer] QDEC question

Dear freesurfer experts, I was able to figure out the problem! I was not supposed to write the eTIV values in my .dat.table which I did and for that reasons my continuous factors were being read as 4 instead of 3. Thanks and regards, Sampada AIIMS, Delhi

Re: [Freesurfer] QDEC question

Dear Freesurfer experts, Thanks for your valuable input. Since, comparison with global thickness does not provide any valuable information we have decided to forego the average thickness and lh-thickness comparison and now added eTIV as another covariate with age ​ and ​ lh/rh thickess ( ​please

[Freesurfer] QDEC question

Dear freesurfer experts, I am trying to do cortical thickness-age correlation in Spinocerebellar ataxia patients (SCA1 and SCA2). ## I successfully ran qcache command on these 10 subjects of SCA1 and SCA2. ##Since my discrete factors are *Gender *(Male and Female) and* Diagnosis* (SCA1 and SCA2),

[Freesurfer] Regarding: Qdec GLM design error

Dear freesurfer experts, I am new to Qdec analysis and I trying to do( using the information provided in the qdec wiki page) group surface analysis in SCA patients 1and 2 and compare their surface thickness using qdec command. The data table is loading successfully but when I go the design and

[Freesurfer] Error Stats Data Import

​Dear free Surfer experts, I am trying to do surface group analysis of 8 patients (for now) divided into two groups of SCA1 and SCA2. wgen I run the qdec command I can get the summary of the data but when I try to generate stats data table I get the following error: [root@localhost qdec]# qdec

Re: [Freesurfer] Regarding: Brainstem substructures

...@nmr.mgh.harvard.edu wrote: Hi Sampada the brainstem stuff was developed after 5.3 so it is likely not in the version you have. Eugenio or Zeke can point you in the right direction. cheers Bruce On Sat, 11 Jul 2015, Dr Sampada Sinha wrote: Dear freesurfer experts, I am trying to do

[Freesurfer] Regarding: Brainstem substructures

Dear freesurfer experts, I am trying to do the brainstem volumetric analysis especially of the medullary region. My recon-all command ran successfully and now when I am trying to run the command ' recon-all -s IMRAN -brainstem-structures' (

Re: [Freesurfer] fslswapdim.fsl: Command not found

extension in the $FREESURFER_HOME/bin directory. Both options are valid. -Zeke On 03/18/2015 06:20 PM, Dr Sampada Sinha wrote: I hope you are looking for this: Last login: Tue Mar 17 15:48:52 on ttys009 rmbp:~ Sampada$ export FREESURFER_HOME=/Applications/freesurfer rmbp:~ Sampada

[Freesurfer] fslswapdim.fsl: Command not found

Hello Freesurfer experts, I am trying to learn dti using data downloaded from the martinis and everything was running fine till I got this message: Wed Mar 18 16:54:54 CDT 2015 --s Diff001 --mov

Re: [Freesurfer] fslswapdim.fsl: Command not found

, Sampada On Wed, Mar 18, 2015 at 5:18 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hello Sampada, Can you please tell me the contents of the build-stamp.txt file in your FREESURFER_HOME directory? -Zeke On 03/18/2015 06:06 PM, Dr Sampada Sinha wrote: Hello Freesurfer experts, I am trying

Re: [Freesurfer] A newbie to fMRI analysis

/User/sampada/Desktop/Vaibhav2/ and then run recon-all S. On Wed, May 14, 2014 7:47 pm, Dr Sampada Sinha wrote: Hello freesurfer, thanks for your message. I am doing the recon-all for T1 and T2* structural dataset now I have in all 8 files in the order of (T2T1T2DTIT@T2*T2). I am

Re: [Freesurfer] A newbie to fMRI analysis

that you can use the tutorials from the freesurfer wiki to do a Feat analysis. For recon_all you need to specify only the subject and the script automatically does the rest. Segmentation and parcellation is automatized (see wiki) Hth, Shantanu On Fri, May 9, 2014 6:26 pm, Dr Sampada Sinha

Re: [Freesurfer] A newbie to fMRI analysis

/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.nii Hth, shantanu On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote: Hello Shantanu, Many thanks for your reply! This is my exact commandline which I give to free surfer for the 1st of the eight nii files. When i

Re: [Freesurfer] A newbie to fMRI analysis

. The 2nd with how you want the data converted. Run it with --help to get more info doug On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file

Re: [Freesurfer] A newbie to fMRI analysis

/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' Regards, Sampada On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh shant...@nmr.mgh.harvard.edu wrote: can you send your exact mri_convert commandline? On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote: *Hello freesurfer* *Sorry

[Freesurfer] A newbie to fMRI analysis

Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the Applications/freesurfer directory. I have run into the first problem and that is of data conversion. My file is in dcm format

Re: [Freesurfer] A newbie to fMRI analysis

files (iyou don't mind me asking that)? I tried changing the location from Desktop to Applications/freesurfer as well, but its still not working. Thanks and regards, Sampada On Mon, Apr 28, 2014 at 8:27 PM, Dr Sampada Sinha drsampadasi...@gmail.comwrote: Hello Shantanu, Thanks for your