[Freesurfer] reconall question

Hello FreeSurfer experts, I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject. While running the FreeSurfer, if I want to use the three mprages for that subject as an input file, may I just keep the three mgz files (001.mgz, 002.mgz and 003.mgz) in the orig

[Freesurfer] recon all question

Hello Freesurfer experts, I am doing volumetrics study. During the scan we get 2-3 mprage per scan for a subject. While running the FreeSurfer, if I want to use the three mprages for that subject as an input file, may I just keep the three mgz files (001.mgz, 002 .mgz and 003.mgz) in

Re: [Freesurfer] recon all question

, September 12, 2013 5:27 PM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all question Hi Rashmi putting them in the orig folder with those numbers will get recon-all to do motion correction and averaging. cheers Bruce On Thu, 12 Sep 2013, Rashmi Singh wrote

Re: [Freesurfer] recon all question

From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, September 13, 2013 8:46 AM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon all question 1. I don't think I know anyone who has done this, and we haven't assessed

Re: [Freesurfer] recon all question

to use this option. Rashmi ___ From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, September 13, 2013 9:09 AM To: Rashmi Singh Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] recon all question what do you want to do

[Freesurfer] Intracranial volume measures

Hello FreeSurfer experts I was looking into the aseg.stat files following reconall runs and found that intracranial volume measurements were really small for some subjects, while other measures were comparable ( example below) May you suggest the reason for that. Cortex vol

[Freesurfer] reconall error

Hello FreeSurfer experts, I am trying to run recon all on my data set, but I got following error message. Please help me understand the message and suggest solution. Thanks, Rashmi #@# Skull Stripping Tue Oct 22 13:57:00 CDT 2013

[Freesurfer] asegstats2table error

Hello, This morning I tried to get the segmentation measurement in table formate, but I got the following error message asegstats2table --subjects AB197.T0b AB232.T0a AD721.T0 --skip --meas volume --tablefile asegstats1.txt Error message :SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the

[Freesurfer] Segmentation question

FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks, Rashmi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Segmentation question

). https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats -Louis On Thu, 7 Nov 2013, Rashmi Singh wrote: FreeSurfer experts, May you please educate me how the supra tentorial volume (STV) measured by FreeSurfer and which date does it take as input file to calculate this variable. Thanks

[Freesurfer] recon all question

Hello FreeSurfer experts, I have a question regarding group analysis and running of recon all group wise. For example I have group A, B, and C with several subjects in each group, if want want to compare their cortical and subcortical measurements group wise, how do I run the recon all. Also

[Freesurfer] Help with Temporal horn

Hello, How can I generate volume for temporal horn, temporal white matter and temporal gray matter. Thanks Rashmi Sent from my iPhone ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Temporal horn measures

Is there any way to get the volume for the temporal horn using FreeSurfer. Thanks, Rashmi ___ 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

Re: [Freesurfer] Temporal horn measures

On Tue, 4 Mar 2014, Rashmi Singh wrote: Is there any way to get the volume for the temporal horn using FreeSurfer. Thanks, Rashmi The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail

Re: [Freesurfer] Temporal horn measures

Thank you Bruce! Rashmi On 3/4/14 12:43 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Rashmi the regions are disjoint, so if you want all temporal lobe you need to add them together. cheers Bruce On Tue, 4 Mar 2014, Rashmi Singh wrote: Thank you Bruce, This is what I had thought

[Freesurfer] urgent help with cortical areas

Hello experts, I have the aparcstat files for corticla thickness. I would want to know is there any information on how may I group these regions more broadly ex frontal , temporal lobe areas. Thanks Rashmi. This document may contain information covered under

[Freesurfer] FreeSurfer Skull Strip issue and longitudinal runs

On Thu, 1 Mar 2012, Rashmi Singh wrote: Hello, I am finding differences in hippocampus voulme of same subject when scanned at different times . Our study requires our subjects to be scanned 3-4 times (T0-T3) within a period of 1 month. We have performed MRI Scanning on all our subjects

Re: [Freesurfer] message bouncing

trouble? You are definitely still on the list. I see. Nick and/or help: can you investigate? thanks Bruce On Thu, 27 Sep 2012, Rashmi Singh wrote: Reply, Yes I started posting since last year, but suddenly after July this year my posts have started bouncing back. That is why I finally

[Freesurfer] Skullstrip error issue

Hello experts, I am getting skull strip issues with FreeSurfer recon-all runs in every data. I ran recon-all on my T1-data and noticed that the skullstrip is not so good. Almost in every subjects there were dura included, so I tried the suggestion of using the flags -skullstrip and -Clean–bm

Re: [Freesurfer] Skullstrip error issue

Rashmi getting rid of all the dura without removing any problem is exceedingly difficult (if not impossible). Usually we live with some remaining dura as it doesn't affect the surface placement much. cheers Bruce On Tue, 2 Oct 2012, Rashmi Singh wrote: Hello experts, I am getting skull strip issues

Re: [Freesurfer] Freesurfer Digest, Vol 108, Issue 12

Hi Melonee, Please record my off Campus work hrs this morning at OU. IN 9:30 AM and out 1:10 PM. I have logged into LIBR when I entered so that should be in records. Let me know if you may have any question. Thanks, Rashmi On 2/11/13 8:39 AM, freesurfer-requ...@nmr.mgh.harvard.edu

[Freesurfer] volumetrics questions

Hello experts, I am doing volumetric studies where I am comparing the subcortical structures volumes among different experimental groups. I usually do two mprages on one subject in a single scan at two time-points. I run recon all on both mprages for a single subjects. To my surprise the

Re: [Freesurfer] volumetrics questions

Rashmi of course they are different - there is noise in the scans and motion and other sources of corruption! The amount of difference will depend on the structure and the quality of the data. cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Hello experts, I am doing volumetric studies

Re: [Freesurfer] volumetrics questions

off picking the better mprage (i.e. less motion) and analyzing it at each timepoint cheers Bruce On Thu, 14 Mar 2013, Rashmi Singh wrote: Thank you Bruce. So what should I do. Shall I just take one of the mprage values or is it a good idea to get the average from two mprages for each

[Freesurfer] Cortical thickness information

the total cortical surface area? Looking forward for your response, Thanks, Rashmi. On 1/18/12 9:18 AM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: On Wed, 18 Jan 2012, Rashmi Singh wrote: Hello, This is Rashmi. I am very new to neurobiology

[Freesurfer] Error message for getting the stat file into table format

Hello, I was trying to get the cortical thickness in the table format for all of my subjects on which I had run recon all. I see the stats folder with rh/lh.aparc.stats files. My command was: aparcstats2table --subjects AA471.T1 AA471.T2 AA471.T3 AA474.T0 AA476.T0 AA479.T0 AA483.T0 AA483.T2

[Freesurfer] how can I view and process Freesurfer files using AFNI

Hello, I ran recon all on my subjects data which went well. Now I would like to use AFNI-SUMA to view it , how do I go about doing this. Thanks, Rashmi. This document may contain information covered under the Privacy Act, 5 USC 552(a), and/or the Health

[Freesurfer] Defects in freesurfer output

Hello, I am getting defects in the volume output of freesurfer with respect to the pial surface and whilte-matter surface boundary. I am wanting to measure the cortical thickness after running recon_all. I was inspecting the pial and white surface using tkmedit and I noticed (volume data

[Freesurfer] Pial and white surface defects.

Hello, I had this issue raised earlier, but may be it got lost in the pile of questions you receive everyday. I am very new to freeSurfer, and may be its me who is dong something wrong so please advise. I am getting defects in the volume output of freesurfer with respect to the pial

[Freesurfer] hippocampus volume normalization question

Hello. I am using FreeSurfer to generate subcortical volumes and cortical thickness for my subjects. Does FreeSurfer normalizes the subcortical volumes to the whole brain volume for each subjects. Let me know. For among subjects comparison I am assuming that the sub cortical volumes

[Freesurfer] significant variation in Hippocampal volume in between scans of same subject

Hello, I am finding differences in hippocampus voulme of same subject when scanned at different times . Our study requires our subjects to be scanned 3-4 times (T0-T3) within a period of 1 month. We have performed MRI Scanning on all our subjects with same sequence using 3T GE scanner.

[Freesurfer] hippocampal segmentation

Hello, I converted the aseg. mgz files to nii format and created a hippcampal mask with 3dcalc. Using AFNI I opened the hippocampal mask as overlay on the brainmask .nii image as underlay. For some subjects the hippocampus is not at the correct position. Please advise. Thanks, Rashmi.

[Freesurfer] recon-all error

Hello, I ran recon –all on my scans and the output files reported the following error: SUBJECTS_DIR /home/rsingh/storage/labs/pbellgowan/MTBI/RASHMIANALYSIS/Check-Long/GE/FreeSurfer FREESURFER_HOME /opt/freesurfer Loading source label. Invalid argument ERROR reading

[Freesurfer] asegstats2table error

Hello, I am trying to get the asegmentation information after the recon-all run in the table form, but I am continuously getting the following error asegstats2table --subjects AA262.G1 AA267.G2 AA304.G1 --meas volume --tablefile asegstats.txt SUBJECTS_DIR : /opt/freesurfer/subjects Parsing the

Re: [Freesurfer] Asegstat2 table error

to copy the list so that others can see the answer and so that others can help with the answer. thanks! doug On 05/16/2012 11:56 AM, Rashmi Singh wrote: Dough, Yes, the stat files exist with all its content. I can individually import the text aseg files into xcell sheet, but I have 44 data

[Freesurfer] longitudinal processing error

Hello, I am running longitudinal stream processing on mprage scans of some subjects who have been scanned multiple times using the same sequence with 32 NOVA channels on GE scanner. For most subjects the base run exited without error, however for few error was reported in the runs. The error