Re: [Freesurfer] SIENAX

We have some cases which we want to process , I searched about SIENAX and as you are more expert in this area, I wanted to know Freesurfer preferences on SIENAX ??? The other thing is process time in these two software. Kind Regards, ___ Freesurfer m

[Freesurfer] SIENAX

Hi, I lately heard about SIENAX and when I looked into it it seems like Freesurfer, using the same brain extraction process and etc. I wanted to ask if it is more complete than Freesurfer or not? and why researcher are going after it? It is for Oxford University I think. Kind Regards, _

Re: [Freesurfer] white surf area

Hello Bruce, Sorry I'm in a hurry and its 3rd time I emailed. What is exactly the feature white surface area and how can I visualize it? Kind regards, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/list

[Freesurfer] lh-Whitesurf

Hello, I couldn't get an answer from you so I will ask my question again: In Freesurfer stats there is a feature named lh-WhiteSurfArea. where is exactly this WhiteSurfArea and how can I show it in freeview on surface or image? Kind Regards, Hassan __

[Freesurfer] lh-WhiteSurfArea

Hello, In Freesurfer stats there is a feature named lh-WhiteSurfArea. where is exactly this WhiteSurfArea and how can I show it in freeview on surface or image? Kind Regards, Hassan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mai

[Freesurfer] .Img format

Hello , I have an image with .img format and an image with .hdr format. Freesurfer cant run them. What im suppose to di0o??? I just want to view the image. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailm

Re: [Freesurfer] recon all erro

Hi emad, I think if you change format type of images to nifti it will work as allright. I had a problem like this and it worked for me... On Dec 24, 2015 8:30 PM, wrote: > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the

[Freesurfer] Region specific stats

Hi everyone, I could get all features from asegstats2table and aparcstats2table, Now I need stats by region, for example frontal lobe stats and etc. How can I get them??? Should I select by myself or there is an easy way? ___ Freesurfer mailing list Fr

[Freesurfer] Supratentorial Volume

Dear all, I have 3 features which i want to display and visualize. -Supratentorial Volume -TotalGrayVol -rh-superiorTemporal Volume how can i do that??? Another thing how can i get the characteristic of these areas like which parts they have in brain and etc. Kind Regrds, ___

[Freesurfer] Recon-all balabels

Hi, I found out how to creat BA labels with command below: recon-all -s -ba-labels and it ran and finished without error, but it didnt create the Ex-Vivo Entorhinal stats. I ran it twice but it just made the BA lables. Kind Regards, ___ Freesurfer m

[Freesurfer] BA lable Error

Hi, Recon-all has error at BA Labels stage. how can i run it from this stage again. I need cortical thickness, Do i need to run it? Kind Regards, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinf

[Freesurfer] recon-all complete in 10 hours!!!!

Hi all, "Recon-all complete in 10 hours,should i be concerned?" I asked this question before, and Bruce said depend on your computer it is acceptable. i checked the hardware, I use virtual box which has 5 cores of cpu and 4GB of RAM. i ran 2 instance of recon-all and both finished within 10 hour

Re: [Freesurfer] Inflated.nofix has holes!!!

About visual inspection!!! Which images should I check??? And how can I understand the defect in images? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-ma

[Freesurfer] Inflated.nofix has holes!!!

Hi All, I have 3 questions: 1- When I check the surfaces by freeview after reconstruction, everything looks fine but the inflated.nofix surface has alot of holes as you can see in the picture ( it is rotated). 2- My subjects finish reconstruction in 10 hours. Is it a problem??? should i be conce

[Freesurfer] Diffrence Between stat files and mris

Hi, I wanted to ask what is the difference between stat files result and the mris_anatomical_stats? can we get the same result using both? i want to get the anatomical thickness of temporal gyruses such as superior temporal gyrus thickness, and non neocortex volumes like hippocamp and amygdala v

[Freesurfer] Dev Version

Hi I downloaded the centos 6 freeview.bin and replaced it into $freesurferhome/bin/freeview.bin but now i cant open freeview, it says that it is not a executable file and it is binary. i wanted to test hippocampal subfields. Kind regards ___ Freesurfer

[Freesurfer] Recon-all Error

Hello, I had the problem which was the recon-all error at "Fix Topology lh" stage for 6 of 12 subjects i ran freesurfer. Bruce then told me to check the lh.orig.nofix and lh.inflated.nofix to see if there is part of skull or cerebellum. But when i want to open them with this command: tkmedit lh.o

[Freesurfer] Hippocamp subfields

Hi, I am using freesurfer v5.3, can I have hippocamp subfields in this version?? Kind regards ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is int

[Freesurfer] Recon all exited with error

Hi, I was running 6 individual and all six couldn't finish at the "Fix Topology lh" . I ran them again but again at this stage they got error. the status file is attached. recon-all-status.log Description: Binary data ___ Freesurfer mailing list Free

[Freesurfer] Dialogs go behind freeview

Dear all, Hi, When i open freeview the images at the center of the screen dont let me see an opne dialog, for example when i want to add surface, the opening dialog go behind them and i cant access the dialog. Kind Regards ___ Freesurfer mailing list Fr

[Freesurfer] Successfull Recon-all

Hi, Finally I could run recon-all with nifti files, dicom couldnt run it showed that recon-all done without errors, but how can i be sure about the quality of the resultws. I ran the tkmedit and tksurfer as the website said! I got the stats too, how can i be sure that stats are correct and

[Freesurfer] Parallel

Hi, Is it possible to run recon-all in parallel for fastening the speed ??? ___ 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

[Freesurfer] ATTACHMENT REMOVED--Recone-all

Please be advised, This message contained one or more of the following prohibited file types: (.zip,.bat,.exe,.pif,.scr). The file(s) have been automatically removed from the message, in order to protect the privacy of our patients and employees, and to protect the integrity of our systems and

Re: [Freesurfer] recon-all

file, and should be a single slice in the correct (i.e. high res T1-weighted) series. Is it in dicom format? cheers Bruce On Sat, 7 Mar 2015, Hassan bakhshi wrote: > Hi? > I'm still stopped at the recon-all stage.? > I use the command correctly and there it is: > > recon-all

[Freesurfer] Recon-all

Hi I'm still stopped at the recon-all stage. I use the command correctly and there it is: recon-all -i /usr/local/139942/I000 -subject test -all the data is a sagital series. I think the command cant be execute at the mri_convert step, because i dont have .mgz files in the test directory.

[Freesurfer] Recon-all (Data for test )

Hi Where can i find data to test freesurfer I want to test recon-all command and then get volume of hippocamp!! Thanks alot ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Th

[Freesurfer] Fwd: Recon-all Error

HI, Im using freesurfer newly, i have a folder of a subject's MRI's named 139942 I tried to run recon-all of a File named I000 The point is to get Superior temporal gyrus thickness. but it show an error and stop working. i looked up archive of FAQ's but i didnt anything usefull. There i