Re: [Freesurfer] Nucleus Accumbens Area or Volume

Hi Bruce, Got it- thank you for clarifying. best, arkadiy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Nucleus Accumbens Area or Volume

Dear Experts, My apologies for the very basic question. I wanted to ask, because it keeps coming up in literature, and I wanted to make sure that I am not mistaken. Based on the documentation, my understanding is that Freesurfer ROI's do not generate Nucleus Accumbens volume, but just NAcc area

[Freesurfer] Diagnosing a recon error

Dear Experts, I was wondering if someone might be able to help diagnose a recon error. I used the following command to initiate recon: recon-all -subject RMD002 -i /ncf/anl/anl01/MultiMode/Data/structural/T1_MEMPRAGE_5_RMD002_e1.nii -T2 /ncf/anl/anl01/MultiMode/Data/structural/T2_SPACE_6_RMD00

Re: [Freesurfer] Recon command with T1 and T2

Got it. Thank you! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Recon command with T1 and T2

Hi Doug, I have a follow up question, if you don’t mind clarifying. My goal is to optimize the reconstruction and increase its accuracy. Would you mind confirming if the flag selection is appropriate for the following scenarios: Multiple T1 scans and one T2 scan: Use the 3T flag and the -T2pial

Re: [Freesurfer] Recon command with T1 and T2

Thank you Doug. Much appreciated. -arkadiy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Recon command with T1 and T2

Dear Experts, I am planning to run "recon" using T1 and T2 images, and was wondering if you wouldn't mind confirming whether this is the right command with recon: recon-all -s ${subject} -i T1.nii -T2 T2.nii -all I have seen a slightly different variation in the mailing archives, but this w

[Freesurfer] hippocampal subfield question

Dear Experts, I was wondering if it is important to wait for the manual edits to be done on a dataset before running hippocampal subfield analyses. I believe that recon-all processing is sufficient, and edits can be done in parallel. But wanted to make sure that they will not affect the nuclei/

Re: [Freesurfer] Best way to update Freeview

Hi everyone, I was able to download Freeview- the link now works. However I am having an issue with starting this version. bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer_6.0/ bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb9

Re: [Freesurfer] Ynt: Ynt: linux data and macbook

In case this is helpful, using a Docker (such as below), might be a helpful solution for reducing cross-platform reproducibility issues: https://mindboggle.readthedocs.io/en/latest/ -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department o

Re: [Freesurfer] Reporting Cohen's D for a significant cluster

Previous Correspondence: Hi Arkadiy can you include the previous correspondance so we have context? And what window did you enter numbers? Was it the left hand side of the info window (under "cursor")? cheers Bruce On Wed, 26 Sep 2018, Maksimovskiy, Arkadiy wrote: Hi Bruce, I

Re: [Freesurfer] Reporting Cohen's D for a significant cluster

Hi Bruce, I wanted to follow up on this as I was unsuccessful in doing what you suggested using Freeview (2.0)- entering numbers into the window does not change anything. Might there be another way to find out the Cohen’s D? Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Post

[Freesurfer] Best way to update Freeview

Dear Experts, Updating Freeview came up as a potential solution for a problem in a different thread, so I posting this as a separate issue, since the question stands on its own. I am currently using “Freeview Version 2.0” – Build Jan 19 2017. This version came with the Freesurfer 6.0 package,

Re: [Freesurfer] Reporting Cohen's D for a significant cluster

Hi Bruce, Thank you so much for the tip and the quick response. For some reason, the position and Cohen’s D value do not change when I input the vertex and I think this might be due to an outdated Freeview version (2.0) that I am using. I attempted to load the new one from this link: https://sur

Re: [Freesurfer] Reporting Cohen's D for a significant cluster

Update: It occurred to me that reporting it for the max verted might be the best idea. In this case, might anyone know what is the best way to navigate the Freeview to a specific vertex number (is there a place where I can input that number). Thanks again. From: "Maksimovskiy, Arkadiy&q

[Freesurfer] Reporting Cohen's D for a significant cluster

Dear Experts, I was requested to report the Cohen’s D value for a significant cluster, which resulted from a cortical thickness analysis. I was able to calculate it and open the resulting Cohen’s D mgh file in Freeview, together with the file, indicating a significant cluster. As expected, when

[Freesurfer] Hippocampal Subfields Logitudinal Processing Error

Dear Experts, I am attempting to initiate a longitudinal portion of the hippocampal subfield module and am getting an error. I was wondering if someone might have a suggestion for troubleshooting. I am using the following version of freesurfer: freesurfer-Darwin-OSX-ElCapitan-dev-20180124-2459

[Freesurfer] -make versus -all for edits

Dear Experts, I was wondering if someone might be able to help me understand what the difference is between the two commands below. It seems that they can be used interchangeably, because I can forsee a situation in which one might not remember which command to run and also have done several typ

[Freesurfer] White matter hypointensities

Dear Experts, I was wondering if anyone might know why the WM hypointensities total number in aseg does not match the sum of left and right white matter hypointensities. Thanks, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Departmen

Re: [Freesurfer] New hippocampal subfields

Hi Eugeno, I am hitting the same error as described in this post, but using a Dev El Capitan version. Here is my error output: [arkadiysnewimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] arkadiy% segmentHA_T1.sh SILVA053 # #@

Re: [Freesurfer] Which Dev Version is Best?

assuming that the changes are mainly patches and additional functions, and should not effect this processing, but wanted to make sure to be safe. Thank you for all of your help and info. -Arkadiy From: "Hoopes, Andrew" Date: Monday, January 22, 2018 at 3:21 PM To: "Maksim

Re: [Freesurfer] Which Dev Version is Best?

to upgrade back up based on your info- might you have any suggestions for how to fix the “cocoa” problem? Thanks again, Arkadiy From: "Hoopes, Andrew" Date: Monday, January 22, 2018 at 2:45 PM To: "Maksimovskiy, Arkadiy" , Freesurfer support list Subject: Re: [Freesurfer]

[Freesurfer] Which Dev Version is Best?

Dear Experts, I was wondering if the OSX-ElCapitan Dev version of freesurfer is only for ElCapital? It has a later date of modification than the “dev” version, so I wanted to check, in case it has new patches. I am running OSX-Sierra, and would love to hear which one would be best. Thank you,

Re: [Freesurfer] Issues with hippo subfields / amygdala fixed

Got it. Thank you so much for all the information. Best, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School ___ Freesurfer mailing list Freesurfer

[Freesurfer] Cloning Voxel Tool Question

Hi All, I was wondering if someone might be able to confirm about whether cloning a voxel is working right based on my description. My concern stems from the fact that when I follow instructions to clone a voxel from a T1 onto the brainmask, I click on the brainmask but do not see any immediate

[Freesurfer] Issues with hippo subfields / amygdala fixed

Dear Dr. Iglesias, Could you please let me know what the specific problems were that are fixed? I am asking because I have already applied this segmentation, and want to make sure that the data is valid. Thank you so much, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow

Re: [Freesurfer] IndexError: list index out of range

Hi Doug, I sent you the tar files, but just wanted to update you that I tried running this with just one subjects and am still getting an error but a different one. The two inputs and output errors in the terminal are pasted below: [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks

Re: [Freesurfer] IndexError: list index out of range

Hi All, I wanted to follow up on this thread because I have been getting a similar type of an error. Here is the info from the terminal: [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] amaksimovskiy% aparcstats2table --subjects SILVA033 SILVA035 SILVA039 SILVA

Re: [Freesurfer] Hippocampal Subfield and Amyg Nuclei ICV Correction

Hi Eugenio, Thank you so much for the helpful information! Best, Arkadiy ___ 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 pe

[Freesurfer] Hippocampal Subfield and Amyg Nuclei ICV Correction

Dear Experts, I have seen this question pop up a few times in the forum, but have not seen a clear response, so I was wondering if someone might be able to clarify or offer their opinion. 1. Do the hippocampal subfields and amygdala nuclei need to be corrected for ICV (either by including

[Freesurfer] Using aparcstats2table for LGI

Dear Experts, I have extracted mean LGI values for each ROI using mri_segstats --annot SUBJ rh aparc --i $SUBJECTS_DIR/SUBJ/surf/rh.pial_lgi --sum lh.aparc.pial_lgi.stats For the next step, I am attempting to combine them into one table, and am trying to use the aparcstats2table function. Does

Re: [Freesurfer] lGI mris_fill Error

Thank you so much for this suggestion. It worked perfectly. I really appreciate all of your help- with this and the previous question. Best, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical Scho

[Freesurfer] lGI mris_fill Error

Dear LGI Experts, I am attempting to run LGI using the freesurfer Dev Version (2017), and am getting the following error: [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks/Post_Manual_Edits] amaksimovskiy% recon-all -s SUBJ002 -localGI INFO: FreeSurfer build stamps do not match Su

Re: [Freesurfer] segmentHA znzread failed error

Thank you so much for your help with this. Much appreciated, * Arkadiy ___ 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 p

Re: [Freesurfer] segmentHA znzread failed error

I verified that it is not a storage issue. Let me know if znzreadInt is important. Thank again, arkadiy From: "Maksimovskiy, Arkadiy" Date: Tuesday, October 24, 2017 at 1:37 PM To: "Freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] segmentHA znzread failed erro

Re: [Freesurfer] segmentHA znzread failed error

znzreadInt: znzread failed znzreadInt: znzread failed znzreadInt: znzread failed znzreadInt: znzread failed Wondering if you might have any suggestions. Checking the storage folders as well. Thanks everyone, arkadiy From: "Maksimovskiy, Arkadiy" Date: Tuesday, October 24, 2017 at

Re: [Freesurfer] segmentHA znzread failed error

Thanks everyone! Doug- I will check the storage. If the outputs look good, is this something to worry about and rerun? Much appreciated, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

[Freesurfer] segmentHA znzread failed error

Dear Hipp. Segmentation experts, I keep getting the following error when running the segmentHA script from the Dev. Version. Wondering if this is serious or something that can be ignored, as the process keeps running to the end: Transforming points znzreadInt: znzread failed No such file or dir

[Freesurfer] Wm edits and wm surface

Hi Everyone, I looked through archived messages, and even though this was mentioned, I did not quiet find a clear response. Is it necessary to make edits to the wm volume if the wm surface is accurate? For example, if the surface follows the wm boundary accurately, but the wm volume has 1. some

[Freesurfer] Freeview Versions

Dear Freesurfer Experts, My apologies if I missed this information elsewhere on the website, but could not find any info. about it. There appear to be two Freeview versions, both from 2017 (released one day apart), for which the screenshots are attached. I was wondering if you could let me kno

[Freesurfer] Combining Echo Frames Error

Dear Freesurfer experts, Here are the commands I entered, and errors I received: recon-all -subjid Test01 -i /Testing/T1_MEMPRAGE_4/IM-0002-0206.dcm -autorecon1 #@# MotionCor Thu Aug 31 09:00:15 EDT 2017 Found 1 runs /Users/amaksimovskiy/Desktop/Testing/Test01/mri/orig/001.mgz Checking for (inv