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Oops ! I am so sorry. I think by the term cog def, you mean cognitive deficit values - got it !
Could you give me some details about how to use binary mask as input in the GLM in FreeSurfer - to do the analysis for both surface and volume?
Thanks.
On Mon, Feb 26, 2024 at 7:16 PM Martin Juneja mj70481@gmail.com wrote:
Hi Doug,
I am glad that I was successful in explaining my goal.
Could you please help me understand: (a) I have completed the recon -all step for all my subjects. What are "cog def" values and how can I calculate those values? (b) How can I run a typical GLM? For my task, should I just follow the steps explained here: https://secure-web.cisco.com/1MlKxXpEDSXPUQ8AZ_j2QuQSHgtcf34xdlZGFWfTNLv8PYa...
I would like to do it on both surface and volume.
Thanks.
On Mon, Feb 26, 2024 at 4:54 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
It sounds like you are just trying to correlate the binary lesion map with cog def values. Basically, a typical GLM where the dependent variable is the binary (0 or 1) mask and the independent variable is the cog def vals. Is that right? If so, do you want to do it on the surface or the volume?
On 2/26/2024 2:17 PM, Martin Juneja wrote:
External Email - Use CautionHi Doug,
No - this has nothing to do with thickness or volume maps. For that, we can just do ROI-wise analysis in FreeSurfer.
For VLSM, here is an example: Let's say I have 10 lesion masks from 10 patients and 10 corresponding subject-wise cognitive deficit values i.e., one value for each subject. I would like to generate a statistical map showing the strength of the relationship between damage at any given voxel (using overlapping sections of those binary masks, maybe) and cognitive deficit across these 10 individuals with lesions. For example, the attached figure from this paper: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/10oYYBbEltAQxasO4HLlCC05qOZRAZ--YSgCb9bq7dN8wyx... https://secure-web.cisco.com/1mkEn3f1Q8GyxmlOPFz7yt7bXXt8EX6B5xDtMifO7EaMNERg0jmEbw8JdjvA1d1mhYY47Aee2RmgM1APG8Qa_L7BA7WRaOj69FtTDv69DjC6tRJssI4IoAwUVliD4mjjXYZStKyi9wEZbBssdKTVUwRLdMJ-kQcPloayCrLfD2GdD81qXtWpyZV97qOn-TNxjm-ri1rdObuPqYYJgsz8YLs_6oL5-j5JkJHhQMvn87uNtF395JrMajc2fp9kFKyWoM1MO3eQed-1WbwwQMGveYqLi3-XXqwMEtJ2qoBkOYMsHotFewuDhuT9szi4C2_XsHdOn_QalRY4JM4iMw0CT6A/https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2213158215300103 gives a spatial/anatomical map showing association between anatomical lesion location and language i.e., it shows what spatial location is significantly associated with language at what significance level.
Please let me know if you need any additional details.
Thanks.
[image: 1-s2.0-S2213158215300103-gr2.jpg]
On Mon, Feb 26, 2024 at 7:59 AM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
Can you be even more specific? Operationally, what does it entail? Are you just trying to correlate, say, cognitive deficits to, say, thickenss?
On 2/25/2024 9:12 PM, Martin Juneja wrote:
External Email - Use CautionHi Doug,
Sorry for not elaborating in my previous email.
Voxel lesion symptom mapping (VLSM) is a method to calculate symptom localization by estimating statistical relationships between damage to specific brain regions (it could be stroke lesion, tumor lesion or TBI lesion etc.) and resulting deficits (e.g., *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1H5g5doZHop8tN6NMLqVe16NVioZ9hVfL6dRElUM8c4w-sK... https://secure-web.cisco.com/1UiWVbssc136ehHR7fbKC3mJg7kJQVmdWhaRoU7E29vpu5yNgNVpd0lZiq4aR019jbUXsgd9ifhWAi0IlkNaX6x9xio5om5mkSpOTNvua1cW-cEEjvzxDi3L2sB29VZVsnhEZ8Tb3UH9P0xee7U6UR5dzGEOh8QJNPNhtL65F1jvipA-Phq6I6tlLdM_es5V3bNy-Uc2GG6yXw2BY9-tSYOxCFzZ8xvUgiqlPE8H6y5TPAXxx9g0S5ELQ2MYBhZc4scdk6uSlw8_4_qsmFzE3pHqfDGZ0Q_Jv3szY1k1AqHkxkI9t7LPh8R6dSgTpNeL4WUyRopXxirT8r-0IxK7nYA/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4724038%2F and *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Ea9VMQdZoS_7sq0gAA7swAgN_6IwQN3ojwhTP1bB4ObVy5... https://secure-web.cisco.com/1Sv3DQt7ECt7yYskA3qSYiurVnqwYgQMrW8bVWoluBQmsM_yLtTYU5rsNedrt7kfxvXWRFNBdsUI4A1g3RXw72SMBIG6ZQrrv9cyiZQGDsnk8bidCzCK_lFen7x0alY7ZhJs5O1HBwG06GFvTNxoPfkbR1hD87w8QzlmPBxoAV_migSoy78DKyb73PilyF7D9vRCcWNAx4UOdo0SSrO_Shf1_py0ygzhtUB2FOJo-0Z-5e1wnn3cKO0-MJMcDUhRdVzUXTYWyey2rVOBEqbKBye_yDzoaxLIKzESNFAVFJGY8t8AlAjZS0kE9aqzZKXXtHqmihL1X2aNJDuA_eQsRZA/https%3A%2F%2Facademic.oup.com%2Fbrain%2Farticle%2F137%2F9%2F2532%2F2848278 ). This method can guide the development of targeted interventions and rehabilitation strategies aimed at improving symptoms by targeting specific brain regions (or networks, if we use network lesion symptom mapping: *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1QPkDRjomOkyPBM-4ZCn7pmLbQHsFaIbwONAreMWCkMvvUX... https://secure-web.cisco.com/10LgUitf4Y4lehNjHOInoyAOPPrjXpKyw8QudhBNFrI-HEs531siCcOCZApchqgDvWDYKy7cM6QODz-i1dQPhiBuCX-00bXDcm2EF8XZrhB_Rknetjx1FVS8u1BBOZ16mMYnGswaNPzNgbt15-7OR0ZajBrz3jJMaAXx2tGeFbJuIT_cwpTPX2u7uVcKu40byzK3CksUD9sBXUODMzo1dWFYJ7dqv9jzjPyhXiM51d49k7iGamx_SlWvcrdjka0R328JXdXbqwiXqt2FEwAVsz1ioBdFbSPNdth73sqgmm1hDt5vQsBMMp8Txr8bGJeZxE6q-ZHf8yqwxiFsXOOVtBw/https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC9724189%2F ).
On Fri, Feb 23, 2024 at 10:27 AM Douglas N. Greve < dgreve@mgh.harvard.edu> wrote:
Sorry, don't know what VLSM is. Can you elaborate?
On 2/6/2024 3:19 PM, Martin Juneja wrote:
External Email - Use CautionDear FreeSurfer community and experts,
I would greatly appreciate any help/response with the following.
Thanks.
---------- Forwarded message --------- From: Martin Juneja mj70481@gmail.com Date: Wed, Jan 31, 2024 at 7:51 PM Subject: Vertex / voxel lesion symptom mapping To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Greetings FreeSurfer community,
I was just wondering if it's possible to perform vertex/voxel lesion symptom mapping (VLSM) using FreeSurfer? In other words, I would like to assess the impact of lesion topography (of course, heterogenous locations across patients) on neurocognitive function in brain tumor patients.
I would greatly appreciate any help/response.
Thanks!
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