Re: [Freesurfer] skull striping error question
Even the Supratentorial volume ? Supratentorial volume includes some structures outside the surfaces ? Thanks Subha - Original Message - From: Bruce Fischl Sent: 10/23/13 01:13 PM To: Subhabrata Chaudhury Subject: Re: [Freesurfer] skull striping error question You should be fine if the surfaces aren't affected by the remaining skull Bruce On Wed, 23 Oct 2013, Subhabrata Chaudhury wrote: > Hi Everyone, > > I have some data where the skull striping hasnt worked properly and there are some skull remaining. > However, upon looking at the white and pial surfaces, those look perfectly fine. My question is will the > erroneous skullstriping affect the supratentorial volume estimation ? > I will be highly obliged if someone can address this concern. > > Regards > > Subha > > 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 contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] skull striping error question
Hi Everyone, I have some data where the skull striping hasnt worked properly and there are some skull remaining. However, upon looking at the white and pial surfaces, those look perfectly fine. My question is will the erroneous skullstriping affect the supratentorial volume estimation ? I will be highly obliged if someone can address this concern. Regards Subha ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] volume of subcortical structure calculation
Hello Where can I get information on how freesurfer calculates volumes of subcortical structures ? Is there a paper which provides insights into this method ? Is it that for certain subcortical structures, it just counts the number of voxels and adds them up since the voxels are 1mm3 ? Thanks Subha ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] 2D smoothing kernel and cluster size
Hi All, When we say FWHM 10, does that mean a circle with a radius of 10 mm ? Also I have some significant clusters from my analysis, will the area of the cluster be in mm2 ? How is the area of a significant cluster calculated ? I mean the math behind it. Is it mapping the cluster to the 1mm3 volume and counting the number of voxels ? (I know I can make a label of the cluster and run the anatomical-stats command to get the value ? Thank you Subha ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] first level glm analysis on surface space
Hello All, I have run recon-all on some subjects. I have functional BOLD data on these subjects too. I am doing fmri preprocessing in spm. I have created register.dat by registering the meanBOLD image to the freesurfer reconstructed data. I am intending to do the following - I want to take each functional volume corresponding to each TR and move each volume to freesurfer and make a BOLD surface file in freesurfer (.mgh file). Then I want to run first level glm on the data like its done for volume data in spm, fsl, afni etc. My question is are there tools in freesurfer to do this on surfaces ? If not, can the mgh file be converted to a gifti file and maybe it can be used to make first level glms in afni, spm or fsl ? I will really appreciate your opinion about this. Thank you very much, Subha ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] combining masks in freesurfer ??
Hello Doug, Thank you. Will fscalc work with volume mask ? You wrote .mgh. mgh is surface data, right ? Best wishes Subha - Original Message - From: Douglas N Greve Sent: 05/30/13 05:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] combining masks in freesurfer ?? you can use fscalc mask1.mgh and mask2.mgh -o mask1-and-mask2.mgz assuming you want to use an AND function doug On 05/30/2013 05:18 PM, Subhabrata Chaudhury wrote: > Hi All, > Is there a way to combine multiple binary volumetric masks into a > single binary volumetric mask in freesurfer ? > Please let me know. > Thankyou > Subha > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] combining masks in freesurfer ??
Hi All, Is there a way to combine multiple binary volumetric masks into a single binary volumetric mask in freesurfer ? Please let me know. Thankyou Subha ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] volume and mean value of a custom made white matter ROI
Hello Everyone, Greetings. I am learning freesurfer tricks. I am stuck and have a question. I have run 10 subjects through freesurfer. I have made custom volume regions for arcuate fasciculus for 10 subjects. Now I want to get some measurements inside this region. How do I get the volume of the region ? How do I get the mean T1 intensity in this region ? Can somebody share some script or point me to some script ? Will be very thankful. Subha ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] averaging lh and rh thickness maps on fsaverage_sym surface
Hi, I want to create an average thickness map of lh and rh. I have run surfreg steps to map lh to lh sym and rh to rh sym. Can you advise what to do next to mke average thickness maps between two hemispheres ? Will either mris_calc or mri_average work to make the average map ? Thank you Subha ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] question about glm setup
Hello Dr. Greve, Thank you for your reply. I have set up the qdec. I have gender as the discrete factor and age and clinical score as continuous factors. In order to look at the relationship between clinical score and whole brain cortical thickness while accounting for age and gender effects, do I select score as the continuous factor and age as the nuisance factor or should it be the other way round ? Thanking you in anticipation, Subha - Original Message - From: Douglas Greve Sent: 05/05/13 11:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] question about glm setup Hi Subha, yes, you can. You will need to create a table in the format with QDEC expects. Have you looked at the tutorial? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis doug On 5/4/13 11:31 AM, Subhabrata Chaudhury wrote: Hi, I am new to freesurfer. I have run reconall on 50 AD subjects. I have also run recon-all -qcache. So I have the following - 1) Whole brain thickness map for each AD subject 2) age of each subject 3) gender of each subject 4) clinical score of each subject I DO NOT have control subjects. I want to run a glm to investigate whether if there is a relation between the clinical score for each subject and their cortical thickness while accounting for age, gender and whole brain average thickness. Can I use qdec for this ? This is my first time doing this sort of analysis, so I will be grateful if I can get some step-by-step help. Thank you very much Subha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] question about glm setup
Hi, I am new to freesurfer. I have run reconall on 50 AD subjects. I have also run recon-all -qcache. So I have the following - 1) Whole brain thickness map for each AD subject 2) age of each subject 3) gender of each subject 4) clinical score of each subject I DO NOT have control subjects. I want to run a glm to investigate whether if there is a relation between the clinical score for each subject and their cortical thickness while accounting for age, gender and whole brain average thickness. Can I use qdec for this ? This is my first time doing this sort of analysis, so I will be grateful if I can get some step-by-step help. Thank you very much Subha ___ 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 person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
